[HELP] LLVM-18.1.7 trashed my EXT4 Journal and probably my SATA Drive too

It seams that LLVM trashed the filesystem Journal and damaged the SATA drive, does any one has a good backup tip that I can use to backup what I have done so far in (B)LFS, I want to avoid having to start all over again.

What happend:

I was running LLVM test suite and got the following error:

[465.624083]EXT4-fs (sda3): failed to convert unwritten extents to written extents -- potential data loss! (inode 1098125, error -30)
FAILED: CMakeFiles/install.util
cd /sources/BLFS/llvm-18.1.7.src/build && /usr/bin/cmake -P cmake_install.cmake
ninja: build stopped: subcommand failed.
ninja: error: remove(.ninja_lock): Read-only file system

Message from syslog@localhost at Sun. Sep 14 00:29:49 2025 ...
kernek: EXT4-fs (sda3):  failed to convert unwritten extents to written extents -- potential data loss! (inode 1098125, error -30)

Message from syslog@localhost at Sun. Sep 14 00:29:49 2025 ...
kernek: EXT4-fs (sda3):  failed to convert unwritten extents to written extents -- potential data loss! (inode 1098125, error -30)

From that day and until today I have tried all I could find online and even tried with ChatGPT but I couldn't recover the file system, neither I could delete the llvm source folder.

I used a livecd to perform the following:

1. fsck:
      fsck.ext4: unable to set superblock flags on /dev/sdc3 /dev/sdc3:***** WARNING: Filesystem still has errors ******
      
      Tried to backup superblocks, all of them failed with the same message:
      
      sudo fsck.ext4 -b 819200 /dev/sdc3 e2fsck 1.47.2 (1-Jan-2025) Superblock needs_recovery flag is clear, but journal has data. Recovery flag not set in backup superblock, so running journal anyway.
      /dev/sdc3: recovering journal Superblock needs_recovery flag is clear, but journal has data. Recovery flag not set in backup superblock, so running journal anyway.
      
      
2. e2fsck (latest version) didn't fix the issue either

3. Check disk health with smartctl

      SATA Phy Event Counters (GP Log 0x11) ID Size Value Description 0x0001 2 0 Command failed due to ICRC error 0x0009 2 1394 Transition from drive PhyRdy to drive PhyNRdy 0x000a 2 1662 Device-to-host register FISes sent due to a COMRESET 0x000b 2 0 CRC errors within host-to-device FIS 0x000d 2 0 Non-CRC errors within host-to-device FIS
      
Changed SATA cable and SATA port in the motherboard and still the issue persisted.

smartctl displays 0 for Reallocated_Sector_Ct, Current_Pending_Sector, and Offline_Uncorrectable.

4. Tried to remove the LLVM source directory using its inode but failed

5. Tried to remove the LLVM source directory using the "find" command, but altough it displayed that the directory was gone it was back when I rebooted the system

6. Tried disable journal → fsck → re-enable journal

      sudo tune2fs -O ^has_journal /dev/sdb3 tune2fs 1.47.3 (8-Jul-2025) Recovering journal. tune2fs: Journal flags inconsistent while recovering journal. Please run e2fsck -fy /dev/sdb3.

      sudo e2fsck -b 32768 -f -y /dev/sdb3 e2fsck 1.47.3 (8-Jul-2025) Superblock needs_recovery flag is clear, but journal has data. Recovery flag not set in backup superblock, so running journal anyway.
      /dev/sdb3: recovering journal Superblock needs_recovery flag is clear, but journal has data. Recovery flag not set in backup superblock, so running journal anyway. Superblock needs_recovery flag is clear, but journal has data. Recovery flag not set in backup superblock, so running journal anyway.
      e2fsck: unable to set superblock flags on /dev/sdb3 /dev/sdb3: ***** FILE SYSTEM WAS MODIFIED *****
      /dev/sdb3: ********** WARNING: Filesystem still has errors **********
      
7. Give up, altought SMART looks "clean" the kernel is logging I/O failures at the hardware level in dmesg

      1. Repeated READ FPDMA QUEUED … timeout errors
      2. ata1: hard resetting link
      3. Unaligned write command
      4. NCQ disabled due to excessive errors
      5. Still ends up with I/O error, dev sda, sector
      
[    3.249195] EXT4-fs (sda3): re-mounted 45d0c6aa-44d4-475b-a366-20c9b4969d04 ro. Quota mode: none.
[   33.414180] ata1.00: exception Emask 0x0 SAct 0x1e0000 SErr 0x0 action 0x6 frozen
[   33.414198] ata1.00: failed command: READ FPDMA QUEUED
[   33.414202] ata1.00: cmd 60/10:88:28:08:00/00:00:00:00:00/40 tag 17 ncq dma 8192 in
                        res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[   33.414218] ata1.00: status: { DRDY }
[   33.414223] ata1.00: failed command: READ FPDMA QUEUED
[   33.414226] ata1.00: cmd 60/30:90:48:08:00/00:00:00:00:00/40 tag 18 ncq dma 24576 in
                        res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[   33.414239] ata1.00: status: { DRDY }
[   33.414244] ata1.00: failed command: READ FPDMA QUEUED
[   33.414247] ata1.00: cmd 60/78:98:88:08:00/00:00:00:00:00/40 tag 19 ncq dma 61440 in
                        res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[   33.414259] ata1.00: status: { DRDY }
[   33.414263] ata1.00: failed command: READ FPDMA QUEUED
[   33.414266] ata1.00: cmd 60/f8:a0:08:09:00/00:00:00:00:00/40 tag 20 ncq dma 126976 in
                        res 40/00:01:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[   33.414278] ata1.00: status: { DRDY }
[   33.414286] ata1: hard resetting link
[   36.682176] ata1: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
[   51.826166] ata1.00: qc timeout after 15000 msecs (cmd 0x47)
[   51.826186] ata1.00: Read log 0x00 page 0x00 failed, Emask 0x4
[   51.826198] ata1.00: configured for UDMA/133
[   51.826205] ata1.00: device reported invalid CHS sector 0
[   51.826210] ata1.00: device reported invalid CHS sector 0
[   51.826213] ata1.00: device reported invalid CHS sector 0
[   52.290176] ata1: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
[   52.294122] ata1.00: configured for UDMA/133
[   52.294131] sd 0:0:0:0: [sda] tag#17 FAILED Result: hostbyte=DID_OK driverbyte=DRIVER_OK cmd_age=49s
[   52.294134] sd 0:0:0:0: [sda] tag#17 Sense Key : Illegal Request [current]
[   52.294136] sd 0:0:0:0: [sda] tag#17 Add. Sense: Unaligned write command
[   52.294139] sd 0:0:0:0: [sda] tag#17 CDB: Read(10) 28 00 00 00 08 28 00 00 10 00
[   52.294140] I/O error, dev sda, sector 2088 op 0x0:(READ) flags 0x80700 phys_seg 1 prio class 0
[   52.294159] sd 0:0:0:0: [sda] tag#18 FAILED Result: hostbyte=DID_OK driverbyte=DRIVER_OK cmd_age=49s
[   52.294161] sd 0:0:0:0: [sda] tag#18 Sense Key : Illegal Request [current]
[   52.294163] sd 0:0:0:0: [sda] tag#18 Add. Sense: Unaligned write command
[   52.294165] sd 0:0:0:0: [sda] tag#18 CDB: Read(10) 28 00 00 00 08 48 00 00 30 00
[   52.294166] I/O error, dev sda, sector 2120 op 0x0:(READ) flags 0x80700 phys_seg 1 prio class 0
[   52.294171] sd 0:0:0:0: [sda] tag#19 FAILED Result: hostbyte=DID_OK driverbyte=DRIVER_OK cmd_age=49s
[   52.294172] sd 0:0:0:0: [sda] tag#19 Sense Key : Illegal Request [current]
[   52.294174] sd 0:0:0:0: [sda] tag#19 Add. Sense: Unaligned write command
[   52.294176] sd 0:0:0:0: [sda] tag#19 CDB: Read(10) 28 00 00 00 08 88 00 00 78 00
[   52.294177] I/O error, dev sda, sector 2184 op 0x0:(READ) flags 0x80700 phys_seg 1 prio class 0
[   52.294182] sd 0:0:0:0: [sda] tag#20 FAILED Result: hostbyte=DID_OK driverbyte=DRIVER_OK cmd_age=49s
[   52.294183] sd 0:0:0:0: [sda] tag#20 Sense Key : Illegal Request [current]
[   52.294185] sd 0:0:0:0: [sda] tag#20 Add. Sense: Unaligned write command
[   52.294187] sd 0:0:0:0: [sda] tag#20 CDB: Read(10) 28 00 00 00 09 08 00 00 f8 00
[   52.294188] I/O error, dev sda, sector 2312 op 0x0:(READ) flags 0x80700 phys_seg 2 prio class 0
[   52.294195] ata1: EH complete
[   52.294373] EXT4-fs (sda3): re-mounted 45d0c6aa-44d4-475b-a366-20c9b4969d04 r/w. Quota mode: none.
[   52.971182] r8169 0000:03:00.0: Direct firmware load for rtl_nic/rtl8168f-1.fw failed with error -2
[   52.971188] r8169 0000:03:00.0: Unable to load firmware rtl_nic/rtl8168f-1.fw (-2)
.
.
.
[   84.606137] ata1.00: exception Emask 0x0 SAct 0x10000 SErr 0x0 action 0x6 frozen
[   84.606155] ata1.00: failed command: READ FPDMA QUEUED
[   84.606159] ata1.00: cmd 60/08:80:00:2f:28/00:00:02:00:00/40 tag 16 ncq dma 4096 in
                        res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[   84.606175] ata1.00: status: { DRDY }
[   84.606184] ata1: hard resetting link
[   87.874140] ata1: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
[   87.878057] ata1.00: configured for UDMA/133
[   87.878062] ata1.00: device reported invalid CHS sector 0
[   87.878069] sd 0:0:0:0: [sda] tag#16 FAILED Result: hostbyte=DID_OK driverbyte=DRIVER_OK cmd_age=33s
[   87.878072] sd 0:0:0:0: [sda] tag#16 Sense Key : Illegal Request [current]
[   87.878075] sd 0:0:0:0: [sda] tag#16 Add. Sense: Unaligned write command
[   87.878077] sd 0:0:0:0: [sda] tag#16 CDB: Read(10) 28 00 02 28 2f 00 00 00 08 00
[   87.878079] I/O error, dev sda, sector 36187904 op 0x0:(READ) flags 0x80700 phys_seg 1 prio class 0
[   87.878085] ata1: EH complete
[  118.406140] ata1.00: exception Emask 0x0 SAct 0x7c000000 SErr 0x0 action 0x6 frozen
[  118.406158] ata1.00: failed command: READ FPDMA QUEUED
[  118.406162] ata1.00: cmd 60/10:d0:00:d8:67/00:00:01:00:00/40 tag 26 ncq dma 8192 in
                        res 40/00:01:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[  118.406178] ata1.00: status: { DRDY }
[  118.406183] ata1.00: failed command: READ FPDMA QUEUED
[  118.406187] ata1.00: cmd 60/18:d8:18:d8:67/00:00:01:00:00/40 tag 27 ncq dma 12288 in
                        res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[  118.406200] ata1.00: status: { DRDY }
[  118.406205] ata1.00: failed command: READ FPDMA QUEUED
[  118.406208] ata1.00: cmd 60/18:e0:38:d8:67/00:00:01:00:00/40 tag 28 ncq dma 12288 in
                        res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[  118.406220] ata1.00: status: { DRDY }
[  118.406225] ata1.00: failed command: READ FPDMA QUEUED
[  118.406228] ata1.00: cmd 60/28:e8:58:d8:67/00:00:01:00:00/40 tag 29 ncq dma 20480 in
                        res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[  118.406240] ata1.00: status: { DRDY }
[  118.406244] ata1.00: failed command: READ FPDMA QUEUED
[  118.406247] ata1.00: cmd 60/38:f0:00:d8:a7/00:00:01:00:00/40 tag 30 ncq dma 28672 in
                        res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[  118.406259] ata1.00: status: { DRDY }
[  118.406265] ata1: hard resetting link
[  118.866142] ata1: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
[  118.870060] ata1.00: configured for UDMA/133
[  118.870064] ata1.00: device reported invalid CHS sector 0
[  118.870065] ata1.00: device reported invalid CHS sector 0
[  118.870067] ata1.00: device reported invalid CHS sector 0
[  118.870068] ata1.00: device reported invalid CHS sector 0
[  118.870073] sd 0:0:0:0: [sda] tag#26 FAILED Result: hostbyte=DID_OK driverbyte=DRIVER_OK cmd_age=30s
[  118.870076] sd 0:0:0:0: [sda] tag#26 Sense Key : Illegal Request [current]
[  118.870078] sd 0:0:0:0: [sda] tag#26 Add. Sense: Unaligned write command
[  118.870080] sd 0:0:0:0: [sda] tag#26 CDB: Read(10) 28 00 01 67 d8 00 00 00 10 00
[  118.870081] I/O error, dev sda, sector 23582720 op 0x0:(READ) flags 0x83700 phys_seg 2 prio class 0
[  118.870089] sd 0:0:0:0: [sda] tag#27 FAILED Result: hostbyte=DID_OK driverbyte=DRIVER_OK cmd_age=30s
[  118.870091] sd 0:0:0:0: [sda] tag#27 Sense Key : Illegal Request [current]
[  118.870092] sd 0:0:0:0: [sda] tag#27 Add. Sense: Unaligned write command
[  118.870094] sd 0:0:0:0: [sda] tag#27 CDB: Read(10) 28 00 01 67 d8 18 00 00 18 00
[  118.870095] I/O error, dev sda, sector 23582744 op 0x0:(READ) flags 0x83700 phys_seg 3 prio class 0
[  118.870100] sd 0:0:0:0: [sda] tag#28 FAILED Result: hostbyte=DID_OK driverbyte=DRIVER_OK cmd_age=30s
[  118.870102] sd 0:0:0:0: [sda] tag#28 Sense Key : Illegal Request [current]
[  118.870103] sd 0:0:0:0: [sda] tag#28 Add. Sense: Unaligned write command
[  118.870105] sd 0:0:0:0: [sda] tag#28 CDB: Read(10) 28 00 01 67 d8 38 00 00 18 00
[  118.870106] I/O error, dev sda, sector 23582776 op 0x0:(READ) flags 0x83700 phys_seg 3 prio class 0
[  118.870110] sd 0:0:0:0: [sda] tag#29 FAILED Result: hostbyte=DID_OK driverbyte=DRIVER_OK cmd_age=30s
[  118.870112] sd 0:0:0:0: [sda] tag#29 Sense Key : Illegal Request [current]
[  118.870114] sd 0:0:0:0: [sda] tag#29 Add. Sense: Unaligned write command
[  118.870115] sd 0:0:0:0: [sda] tag#29 CDB: Read(10) 28 00 01 67 d8 58 00 00 28 00
[  118.870116] I/O error, dev sda, sector 23582808 op 0x0:(READ) flags 0x83700 phys_seg 5 prio class 0
[  118.870121] sd 0:0:0:0: [sda] tag#30 FAILED Result: hostbyte=DID_OK driverbyte=DRIVER_OK cmd_age=30s
[  118.870122] sd 0:0:0:0: [sda] tag#30 Sense Key : Illegal Request [current]
[  118.870124] sd 0:0:0:0: [sda] tag#30 Add. Sense: Unaligned write command
[  118.870126] sd 0:0:0:0: [sda] tag#30 CDB: Read(10) 28 00 01 a7 d8 00 00 00 38 00
[  118.870127] I/O error, dev sda, sector 27777024 op 0x0:(READ) flags 0x83700 phys_seg 7 prio class 0
[  118.870131] ata1: EH complete
[  149.123173] ata1.00: NCQ disabled due to excessive errors
[  149.123182] ata1.00: exception Emask 0x0 SAct 0x100 SErr 0x0 action 0x6 frozen
[  149.123193] ata1.00: failed command: READ FPDMA QUEUED
[  149.123197] ata1.00: cmd 60/38:40:20:2a:64/00:00:01:00:00/40 tag 8 ncq dma 28672 in
                        res 40/00:00:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[  149.123212] ata1.00: status: { DRDY }
[  149.123221] ata1: hard resetting link
[  149.586142] ata1: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
[  149.590055] ata1.00: configured for UDMA/133
[  149.590059] ata1.00: device reported invalid CHS sector 0
[  149.590064] sd 0:0:0:0: [sda] tag#8 FAILED Result: hostbyte=DID_OK driverbyte=DRIVER_OK cmd_age=30s
[  149.590067] sd 0:0:0:0: [sda] tag#8 Sense Key : Illegal Request [current]
[  149.590069] sd 0:0:0:0: [sda] tag#8 Add. Sense: Unaligned write command
[  149.590071] sd 0:0:0:0: [sda] tag#8 CDB: Read(10) 28 00 01 64 2a 20 00 00 38 00
[  149.590073] I/O error, dev sda, sector 23341600 op 0x0:(READ) flags 0x80700 phys_seg 6 prio class 0
[  149.590090] ata1: EH complete
[  332.914295] kworker/0:1 (9) used greatest stack depth: 11280 bytes left

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