How to restore a LUKS 2 drive corrupt by improper partition resizing?

Question

I have a 256 GB (232.88 GiB) M.2 SSD with GPT and a root partition which is a "full-drive" LUKS 2. The drive actually has some unencrypted partitions too - bootloader w/ cryptsetup, recovery & swap. This drive has Pop!_OS 20.04 installed on it.

Recenly I tried to shrink the LUKS 2 encrypted root partition (to allocate mote space to swap) from a live-USB Artix Linux w/ KDE Plasma's KDE Partition Manager. Here's the steps I've done (Notice: All the actions were performed in KDE Partition Manager via GUI):

1. I've unencrypted ("unlocked", decrypted w/ password) the LUKS 2 partition at /dev/sda3 (which is 224.40 GiB in size, and it had only 158.36 GiB used);
2. I've opened the "unlocked" partition's mapper device in KDE Partition Manager (in my case it was at path /dev/data_h3LfB);
3. I've shrinked the volume of the root partition "inside" the LUKS container at the tail of it (from the right, at the end) to the 208.38 GiB, supposedly freeing 16 GiB;
4. I've saved the changs successfully;
5. I've tried to resize the partition again (because I needed some more space for swap), but the app started to give me an error:

Job: Check file system on partition ‘/dev/data_h3LfB/root’ 
Command: e2fsck -f -y -v /dev/data_h3LfB/root 
Check file system on partition ‘/dev/data_h3LfB/root’: Error

Checking partition ‘/dev/data_h3LfB/root’ before resize/move failed. 

Here are some logs and debug info:

# cryptsetup luksDump /dev/sda3

LUKS header information
Version:        2
Epoch:          3
Metadata area:  16384 [bytes]
Keyslots area:  16744448 [bytes]
UUID:           d0d243ca-cced-4759-acc1-4fdb807726d6
Label:          (no label)
Subsystem:      (no subsystem)
Flags:          (no flags)

Data segments:
  0: crypt
    offset: 16777216 [bytes]
    length: (whole device)
    cipher: aes-xts-plain64
    sector: 512 [bytes]

Keyslots:
  0: luks2
    Key:        512 bits
    Priority:   normal
    Cipher:     aes-xts-plain64
    Cipher key: 512 bits
    PBKDF:      argon2i
    Time cost:  4
    Memory:     1048576
    Threads:    4
    Salt:       70 9c 8e 05 5d 36 b2 df cb 25 05 2b d9 98 a9 91 
                dc 0e 2a 39 2f c0 b0 89 50 a4 e4 8c ed 53 d8 ff 
    AF stripes: 4000
    AF hash:    sha256
    Area offset:32768 [bytes]
    Area length:258048 [bytes]
    Digest ID:  0
Tokens:
Digests:
  0: pbkdf2
    Hash:       sha256
    Iterations: 107084
    Salt:       66 e8 02 be 6b f0 b4 b3 7c 51 43 16 95 0d f0 11 
                41 c2 d2 4b c9 72 f4 95 c6 d7 e9 4f 18 aa 8a c7 
    Digest:     b7 45 38 83 7b 94 66 5e 62 a5 c9 46 71 a2 25 4d 
                dc a5 05 6d 23 98 6f fc 4f 5b ae 32 89 ec 5d 32

# hexdump -C -n 16416 /dev/sda3

00000000  4c 55 4b 53 ba be 00 02  00 00 00 00 00 00 40 00  |LUKS..........@.|
00000010  00 00 00 00 00 00 00 03  00 00 00 00 00 00 00 00  |................|
00000020  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
*
00000040  00 00 00 00 00 00 00 00  73 68 61 32 35 36 00 00  |........sha256..|
00000050  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000060  00 00 00 00 00 00 00 00  cd 12 ab c1 70 ae f1 f0  |............p...|
00000070  ea a9 85 7b dc 3f f8 33  3e 89 b6 38 a0 06 f1 19  |...{.?.3>..8....|
00000080  cc 93 ba 84 e6 a5 55 72  10 6a cc 8d 16 f7 59 10  |......Ur.j....Y.|
00000090  b8 cd 5f 7e 65 75 57 9a  69 b2 87 aa 94 75 7e 98  |.._~euW.i....u~.|
000000a0  a1 2a f8 60 1f 3c 04 17  64 30 64 32 34 33 63 61  |.*.`.<..d0d243ca|
000000b0  2d 63 63 65 64 2d 34 37  35 39 2d 61 63 63 31 2d  |-cced-4759-acc1-|
000000c0  34 66 64 62 38 30 37 37  32 36 64 36 00 00 00 00  |4fdb807726d6....|
000000d0  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
*
000001c0  49 8c be 50 d4 2d 5b e4  f1 b8 44 6d 11 be 4f 80  |I..P.-[...Dm..O.|
000001d0  a8 85 1e a0 d5 e3 99 8e  57 a2 78 59 a3 b4 29 76  |........W.xY..)v|
000001e0  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
*
00001000  7b 22 6b 65 79 73 6c 6f  74 73 22 3a 7b 22 30 22  |{"keyslots":{"0"|
00001010  3a 7b 22 74 79 70 65 22  3a 22 6c 75 6b 73 32 22  |:{"type":"luks2"|
00001020  2c 22 6b 65 79 5f 73 69  7a 65 22 3a 36 34 2c 22  |,"key_size":64,"|
00001030  61 66 22 3a 7b 22 74 79  70 65 22 3a 22 6c 75 6b  |af":{"type":"luk|
00001040  73 31 22 2c 22 73 74 72  69 70 65 73 22 3a 34 30  |s1","stripes":40|
00001050  30 30 2c 22 68 61 73 68  22 3a 22 73 68 61 32 35  |00,"hash":"sha25|
00001060  36 22 7d 2c 22 61 72 65  61 22 3a 7b 22 74 79 70  |6"},"area":{"typ|
00001070  65 22 3a 22 72 61 77 22  2c 22 6f 66 66 73 65 74  |e":"raw","offset|
00001080  22 3a 22 33 32 37 36 38  22 2c 22 73 69 7a 65 22  |":"32768","size"|
00001090  3a 22 32 35 38 30 34 38  22 2c 22 65 6e 63 72 79  |:"258048","encry|
000010a0  70 74 69 6f 6e 22 3a 22  61 65 73 2d 78 74 73 2d  |ption":"aes-xts-|
000010b0  70 6c 61 69 6e 36 34 22  2c 22 6b 65 79 5f 73 69  |plain64","key_si|
000010c0  7a 65 22 3a 36 34 7d 2c  22 6b 64 66 22 3a 7b 22  |ze":64},"kdf":{"|
000010d0  74 79 70 65 22 3a 22 61  72 67 6f 6e 32 69 22 2c  |type":"argon2i",|
000010e0  22 74 69 6d 65 22 3a 34  2c 22 6d 65 6d 6f 72 79  |"time":4,"memory|
000010f0  22 3a 31 30 34 38 35 37  36 2c 22 63 70 75 73 22  |":1048576,"cpus"|
00001100  3a 34 2c 22 73 61 6c 74  22 3a 22 63 4a 79 4f 42  |:4,"salt":"cJyOB|
00001110  56 30 32 73 74 2f 4c 4a  51 55 72 32 5a 69 70 6b  |V02st/LJQUr2Zipk|
00001120  64 77 4f 4b 6a 6b 76 77  4c 43 4a 55 4b 54 6b 6a  |dwOKjkvwLCJUKTkj|
00001130  4f 31 54 32 50 38 3d 22  7d 7d 7d 2c 22 74 6f 6b  |O1T2P8="}}},"tok|
00001140  65 6e 73 22 3a 7b 7d 2c  22 73 65 67 6d 65 6e 74  |ens":{},"segment|
00001150  73 22 3a 7b 22 30 22 3a  7b 22 74 79 70 65 22 3a  |s":{"0":{"type":|
00001160  22 63 72 79 70 74 22 2c  22 6f 66 66 73 65 74 22  |"crypt","offset"|
00001170  3a 22 31 36 37 37 37 32  31 36 22 2c 22 73 69 7a  |:"16777216","siz|
00001180  65 22 3a 22 64 79 6e 61  6d 69 63 22 2c 22 69 76  |e":"dynamic","iv|
00001190  5f 74 77 65 61 6b 22 3a  22 30 22 2c 22 65 6e 63  |_tweak":"0","enc|
000011a0  72 79 70 74 69 6f 6e 22  3a 22 61 65 73 2d 78 74  |ryption":"aes-xt|
000011b0  73 2d 70 6c 61 69 6e 36  34 22 2c 22 73 65 63 74  |s-plain64","sect|
000011c0  6f 72 5f 73 69 7a 65 22  3a 35 31 32 7d 7d 2c 22  |or_size":512}},"|
000011d0  64 69 67 65 73 74 73 22  3a 7b 22 30 22 3a 7b 22  |digests":{"0":{"|
000011e0  74 79 70 65 22 3a 22 70  62 6b 64 66 32 22 2c 22  |type":"pbkdf2","|
000011f0  6b 65 79 73 6c 6f 74 73  22 3a 5b 22 30 22 5d 2c  |keyslots":["0"],|
00001200  22 73 65 67 6d 65 6e 74  73 22 3a 5b 22 30 22 5d  |"segments":["0"]|
00001210  2c 22 68 61 73 68 22 3a  22 73 68 61 32 35 36 22  |,"hash":"sha256"|
00001220  2c 22 69 74 65 72 61 74  69 6f 6e 73 22 3a 31 30  |,"iterations":10|
00001230  37 30 38 34 2c 22 73 61  6c 74 22 3a 22 5a 75 67  |7084,"salt":"Zug|
00001240  43 76 6d 76 77 74 4c 4e  38 55 55 4d 57 6c 51 33  |CvmvwtLN8UUMWlQ3|
00001250  77 45 55 48 43 30 6b 76  4a 63 76 53 56 78 74 66  |wEUHC0kvJcvSVxtf|
00001260  70 54 78 69 71 69 73 63  3d 22 2c 22 64 69 67 65  |pTxiqisc=","dige|
00001270  73 74 22 3a 22 74 30 55  34 67 33 75 55 5a 6c 35  |st":"t0U4g3uUZl5|
00001280  69 70 63 6c 47 63 61 49  6c 54 64 79 6c 42 57 30  |ipclGcaIlTdylBW0|
00001290  6a 6d 47 2f 38 54 31 75  75 4d 6f 6e 73 58 54 49  |jmG/8T1uuMonsXTI|
000012a0  3d 22 7d 7d 2c 22 63 6f  6e 66 69 67 22 3a 7b 22  |="}},"config":{"|
000012b0  6a 73 6f 6e 5f 73 69 7a  65 22 3a 22 31 32 32 38  |json_size":"1228|
000012c0  38 22 2c 22 6b 65 79 73  6c 6f 74 73 5f 73 69 7a  |8","keyslots_siz|
000012d0  65 22 3a 22 31 36 37 34  34 34 34 38 22 7d 7d 00  |e":"16744448"}}.|
000012e0  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
*
00004000  53 4b 55 4c ba be 00 02  00 00 00 00 00 00 40 00  |SKUL..........@.|
00004010  00 00 00 00 00 00 00 03  00 00 00 00 00 00 00 00  |................|
00004020  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|

# dmesg

[ 6703.195671] EXT4-fs (dm-1): bad geometry: block count 58819584 exceeds size of device (54624256 blocks)

# gdisk

GPT fdisk (gdisk) version 1.0.9

Type device filename, or press <Enter> to exit: /dev/data_h3LfB/root
Partition table scan:
  MBR: not present
  BSD: not present
  APM: not present
  GPT: not present

Creating new GPT entries in memory.

Command (? for help): p
Disk /dev/data_h3LfB/root: 436994048 sectors, 208.4 GiB
Sector size (logical/physical): 512/512 bytes
Disk identifier (GUID): 27F0C8A2-A959-4875-BC02-5E7234CBB5C3
Partition table holds up to 128 entries
Main partition table begins at sector 2 and ends at sector 33
First usable sector is 34, last usable sector is 436994014
Partitions will be aligned on 2048-sector boundaries
Total free space is 436993981 sectors (208.4 GiB)

Number  Start (sector)    End (sector)  Size       Code  Name

# e2fsck /dev/data_h3LfB/root

e2fsck 1.46.5 (30-Dec-2021)
The filesystem size (according to the superblock) is 58819584 blocks
The physical size of the device is 54624256 blocks
Either the superblock or the partition table is likely to be corrupt!
Abort<y>? yes

# lvdisplay

  --- Logical volume ---
  LV Path                /dev/data_h3LfB/root
  LV Name                root
  VG Name                data_h3LfB
  LV UUID                IieMpP-a4AZ-5NCr-jp7O-YxRX-iIIp-Rk9UJU
  LV Write Access        read/write
  LV Creation host, time pop-os, 2020-11-24 00:54:18 +0500
  LV Status              available
  # open                 0
  LV Size                <208.38 GiB
  Current LE             53344
  Segments               1
  Allocation             inherit
  Read ahead sectors     auto
  - currently set to     256
  Block device           254:1

# vgdisplay

  --- Volume group ---
  VG Name               data_h3LfB
  System ID             
  Format                lvm2
  Metadata Areas        1
  Metadata Sequence No  3
  VG Access             read/write
  VG Status             resizable
  MAX LV                0
  Cur LV                1
  Open LV               1
  Max PV                0
  Cur PV                1
  Act PV                1
  VG Size               <224.38 GiB
  PE Size               4.00 MiB
  Total PE              57441
  Alloc PE / Size       53344 / <208.38 GiB
  Free  PE / Size       4097 / 16.00 GiB
  VG UUID               yj7JnE-u3OE-4hGA-v7cv-14dt-U9Xh-yGtRww

LUKS header seems to be fine.

# fdisk /dev/data_h3LfB/root

Welcome to fdisk (util-linux 2.38).
Changes will remain in memory only, until you decide to write them.
Be careful before using the write command.

The device contains 'ext4' signature and it will be removed by a write command. See fdisk(8) man page and --wipe option for more details.

Device does not contain a recognized partition table.
Created a new DOS disklabel with disk identifier 0xb8237d87.

Command (m for help): p
Disk /dev/data_h3LfB/root: 208.38 GiB, 223740952576 bytes, 436994048 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xb8237d87

Command (m for help): F
Unpartitioned space /dev/data_h3LfB/root: 208.37 GiB, 223739904000 bytes, 436992000 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes

Start       End   Sectors   Size
 2048 436994047 436992000 208.4G

Fdisk doesn't recognize the partition as partition and free space as free space.

Is data lost or is it still recoverable? How do I restore it? Where is partition table stored for LUKS 2 partitions? Is it possible to "uncorrupt" it manually?

Answer 1

lvextend --extents +100%FREE /dev/mapper/data_h3LfB-root fixed everything for me.

More here.