Ugh. I think my USB controller in my computer is failing (or it might be loose, but I don't think my cable is bad) too (the SD card in the Kobo is fine). I'm going to switch back to my laptop and try the sqlite recovery again. Note that the FS was working fine before (plus, I've been accessing my Kobo from my laptop until this time anyways), and I did that integrity check over telnet on the Kobo itself.
Code:
[98335.121682] usb 1-4.3: reset high-speed USB device number 13 using xhci_hcd
[98340.149417] usb 1-4.3: can't restore configuration #1 (error=-110)
[98340.149651] usb 1-4.3: USB disconnect, device number 13
[98340.165285] blk_update_request: I/O error, dev sdd, sector 0 op 0x1:(WRITE) flags 0x800 phys_seg 0 prio class 0
[98340.165363] blk_update_request: I/O error, dev sdd, sector 1 op 0x1:(WRITE) flags 0x100000 phys_seg 1 prio class 0
[98340.165367] Buffer I/O error on dev sdd, logical block 1, lost async page write
[98340.165381] blk_update_request: I/O error, dev sdd, sector 28064 op 0x1:(WRITE) flags 0x100000 phys_seg 2 prio class 0
[98340.165383] Buffer I/O error on dev sdd, logical block 28064, lost async page write
[98340.165384] Buffer I/O error on dev sdd, logical block 28065, lost async page write
[98340.165393] blk_update_request: I/O error, dev sdd, sector 28065 op 0x0:(READ) flags 0x0 phys_seg 1 prio class 0
[98340.165409] FAT-fs (sdd): unable to read inode block for updating (i_pos 449044)
[98340.177961] ------------[ cut here ]------------
[98340.177962] bdi-block not registered
[98340.177981] WARNING: CPU: 1 PID: 654183 at fs/fs-writeback.c:2321 __mark_inode_dirty+0x177/0x380
[98340.177981] Modules linked in: fuse snd_seq xt_nat veth nf_conntrack_netlink xfrm_user xfrm_algo xt_addrtype br_netfilter overlay ctr ccm xt_MASQUERADE xt_conntrack xt_CHECKSUM ipt_REJECT nf_reject_ipv4 xt_tcpudp nft_compat nft_chain_nat nf_nat nf_conntrack nf_defrag_ipv6 nf_defrag_ipv4 libcrc32c nft_counter tun bridge stp llc nf_tables nfnetlink binfmt_misc nls_ascii nls_cp437 vfat fat intel_rapl_msr hid_logitech_hidpp intel_rapl_common x86_pkg_temp_thermal intel_powerclamp coretemp kvm_intel joydev kvm irqbypass rtsx_usb_sdmmc mei_wdt mmc_core rtsx_usb_ms memstick iTCO_wdt iTCO_vendor_support watchdog wmi_bmof crct10dif_pclmul iwlmvm crc32_pclmul mac80211 ghash_clmulni_intel libarc4 snd_hda_codec_realtek intel_cstate intel_uncore snd_hda_codec_generic efi_pstore intel_rapl_perf ledtrig_audio iwlwifi snd_hda_codec_hdmi efivars pcspkr snd_hda_intel i2c_i801 snd_intel_dspcfg sr_mod snd_usb_audio uas cdrom snd_hda_codec snd_usbmidi_lib usb_storage snd_rawmidi cfg80211 snd_hda_core
[98340.178004] snd_seq_device mc snd_hwdep hid_logitech_dj rtsx_usb snd_pcm lpc_ich ehci_pci e1000e sg rfkill snd_timer ehci_hcd mei_me mfd_core ptp mei snd pps_core soundcore wmi button parport_pc ppdev lp parport efivarfs ip_tables x_tables autofs4 ext4 crc16 mbcache jbd2 crc32c_generic hid_generic usbhid hid sd_mod evdev i915 crc32c_intel ahci libahci aesni_intel libata i2c_algo_bit glue_helper drm_kms_helper crypto_simd cryptd xhci_pci scsi_mod xhci_hcd drm usbcore usb_common fan video
[98340.178021] CPU: 1 PID: 654183 Comm: sqlite3 Not tainted 5.5.0-2-amd64 #1 Debian 5.5.17-1
[98340.178022] Hardware name: Acer Aspire TC-603/Aspire TC-603, BIOS P11-B0 10/17/2014
[98340.178023] RIP: 0010:__mark_inode_dirty+0x177/0x380
[98340.178024] Code: 8f f0 ff ff 49 89 c4 48 8b 00 f6 40 5c 02 75 1c 49 8b 54 24 08 83 e2 01 75 12 48 8b 70 50 48 c7 c7 80 78 af 82 e8 cb 9d db ff <0f> 0b 48 8b 05 a0 bf d3 00 48 89 85 c8 00 00 00 45 85 ff 74 0e 48
[98340.178025] RSP: 0018:ffffaf96485abd40 EFLAGS: 00010286
[98340.178026] RAX: 0000000000000000 RBX: 0000000000000003 RCX: 0000000000000007
[98340.178026] RDX: 0000000000000007 RSI: 0000000000000096 RDI: ffff8ca153299a40
[98340.178027] RBP: ffff8c9f4c760368 R08: 0000000000000762 R09: 0000000000000004
[98340.178027] R10: 0000000000000000 R11: 0000000000000001 R12: ffff8ca12545ec78
[98340.178028] R13: ffff8c9f4c7603f0 R14: 0000000000000000 R15: 0000000000000000
[98340.178029] FS: 00007fa8e969a740(0000) GS:ffff8ca153280000(0000) knlGS:0000000000000000
[98340.178029] CS: 0010 DS: 0000 ES: 0000 CR0: 0000000080050033
[98340.178030] CR2: 000055fc3b321360 CR3: 00000002b297e005 CR4: 00000000001606e0
[98340.178030] Call Trace:
[98340.178037] fat_truncate_blocks+0xda/0x300 [fat]
[98340.178040] ? _cond_resched+0x15/0x30
[98340.178041] ? down_write+0xe/0x40
[98340.178044] ? unmap_mapping_pages+0x5e/0x130
[98340.178045] fat_setattr+0x300/0x310 [fat]
[98340.178048] notify_change+0x33b/0x4a0
[98340.178050] do_truncate+0x76/0xd0
[98340.178052] do_sys_ftruncate+0x12f/0x180
[98340.178054] do_syscall_64+0x52/0x180
[98340.178055] entry_SYSCALL_64_after_hwframe+0x44/0xa9
[98340.178057] RIP: 0033:0x7fa8e97c48f7
[98340.178058] Code: 77 01 c3 48 8b 15 99 55 0c 00 f7 d8 64 89 02 b8 ff ff ff ff c3 66 2e 0f 1f 84 00 00 00 00 00 0f 1f 40 00 b8 4d 00 00 00 0f 05 <48> 3d 00 f0 ff ff 77 01 c3 48 8b 15 69 55 0c 00 f7 d8 64 89 02 b8
[98340.178059] RSP: 002b:00007ffc7eb4ab48 EFLAGS: 00000246 ORIG_RAX: 000000000000004d
[98340.178060] RAX: ffffffffffffffda RBX: 0000000000000000 RCX: 00007fa8e97c48f7
[98340.178060] RDX: 000000000281f000 RSI: 0000000000000000 RDI: 0000000000000003
[98340.178061] RBP: 0000000000000003 R08: 0000000000000001 R09: 0000000000000400
[98340.178061] R10: 0000000000000018 R11: 0000000000000246 R12: 0000000000000000
[98340.178062] R13: 0000000000001000 R14: 0000000000000000 R15: 0000000000001000
[98340.178063] ---[ end trace 0f002bfb0ca96f0d ]---
[98340.178072] FAT-fs (sdd): FAT read failed (blocknr 12069)
[98340.178077] FAT-fs (sdd): unable to read inode block for updating (i_pos 449041)
[98340.178079] ------------[ cut here ]------------
[98340.178079] bdi-block not registered
[98340.178082] WARNING: CPU: 1 PID: 654183 at fs/fs-writeback.c:2321 __mark_inode_dirty+0x177/0x380
[98340.178082] Modules linked in: fuse snd_seq xt_nat veth nf_conntrack_netlink xfrm_user xfrm_algo xt_addrtype br_netfilter overlay ctr ccm xt_MASQUERADE xt_conntrack xt_CHECKSUM ipt_REJECT nf_reject_ipv4 xt_tcpudp nft_compat nft_chain_nat nf_nat nf_conntrack nf_defrag_ipv6 nf_defrag_ipv4 libcrc32c nft_counter tun bridge stp llc nf_tables nfnetlink binfmt_misc nls_ascii nls_cp437 vfat fat intel_rapl_msr hid_logitech_hidpp intel_rapl_common x86_pkg_temp_thermal intel_powerclamp coretemp kvm_intel joydev kvm irqbypass rtsx_usb_sdmmc mei_wdt mmc_core rtsx_usb_ms memstick iTCO_wdt iTCO_vendor_support watchdog wmi_bmof crct10dif_pclmul iwlmvm crc32_pclmul mac80211 ghash_clmulni_intel libarc4 snd_hda_codec_realtek intel_cstate intel_uncore snd_hda_codec_generic efi_pstore intel_rapl_perf ledtrig_audio iwlwifi snd_hda_codec_hdmi efivars pcspkr snd_hda_intel i2c_i801 snd_intel_dspcfg sr_mod snd_usb_audio uas cdrom snd_hda_codec snd_usbmidi_lib usb_storage snd_rawmidi cfg80211 snd_hda_core
[98340.178094] snd_seq_device mc snd_hwdep hid_logitech_dj rtsx_usb snd_pcm lpc_ich ehci_pci e1000e sg rfkill snd_timer ehci_hcd mei_me mfd_core ptp mei snd pps_core soundcore wmi button parport_pc ppdev lp parport efivarfs ip_tables x_tables autofs4 ext4 crc16 mbcache jbd2 crc32c_generic hid_generic usbhid hid sd_mod evdev i915 crc32c_intel ahci libahci aesni_intel libata i2c_algo_bit glue_helper drm_kms_helper crypto_simd cryptd xhci_pci scsi_mod xhci_hcd drm usbcore usb_common fan video
[98340.178102] CPU: 1 PID: 654183 Comm: sqlite3 Tainted: G W 5.5.0-2-amd64 #1 Debian 5.5.17-1
[98340.178103] Hardware name: Acer Aspire TC-603/Aspire TC-603, BIOS P11-B0 10/17/2014
[98340.178103] RIP: 0010:__mark_inode_dirty+0x177/0x380
[98340.178105] Code: 8f f0 ff ff 49 89 c4 48 8b 00 f6 40 5c 02 75 1c 49 8b 54 24 08 83 e2 01 75 12 48 8b 70 50 48 c7 c7 80 78 af 82 e8 cb 9d db ff <0f> 0b 48 8b 05 a0 bf d3 00 48 89 85 c8 00 00 00 45 85 ff 74 0e 48
[98340.178105] RSP: 0018:ffffaf96485abdc0 EFLAGS: 00010282
[98340.178106] RAX: 0000000000000000 RBX: 0000000000000003 RCX: 0000000000000007
[98340.178106] RDX: 0000000000000007 RSI: 0000000000000092 RDI: ffff8ca153299a40
[98340.178107] RBP: ffff8c9f4c760368 R08: 000000000000078a R09: 0000000000000004
[98340.178107] R10: 0000000000000000 R11: 0000000000000001 R12: ffff8ca12545ec78
[98340.178108] R13: ffff8c9f4c7603f0 R14: 0000000000000000 R15: 0000000000000000
[98340.178108] FS: 00007fa8e969a740(0000) GS:ffff8ca153280000(0000) knlGS:0000000000000000
[98340.178109] CS: 0010 DS: 0000 ES: 0000 CR0: 0000000080050033
[98340.178109] CR2: 000055fc3b321360 CR3: 00000002b297e005 CR4: 00000000001606e0
[98340.178110] Call Trace:
[98340.178112] fat_setattr+0x1c1/0x310 [fat]
[98340.178113] notify_change+0x33b/0x4a0
[98340.178114] do_truncate+0x76/0xd0
[98340.178116] do_sys_ftruncate+0x12f/0x180
[98340.178117] do_syscall_64+0x52/0x180
[98340.178118] entry_SYSCALL_64_after_hwframe+0x44/0xa9
[98340.178119] RIP: 0033:0x7fa8e97c48f7
[98340.178120] Code: 77 01 c3 48 8b 15 99 55 0c 00 f7 d8 64 89 02 b8 ff ff ff ff c3 66 2e 0f 1f 84 00 00 00 00 00 0f 1f 40 00 b8 4d 00 00 00 0f 05 <48> 3d 00 f0 ff ff 77 01 c3 48 8b 15 69 55 0c 00 f7 d8 64 89 02 b8
[98340.178120] RSP: 002b:00007ffc7eb4ab48 EFLAGS: 00000246 ORIG_RAX: 000000000000004d
[98340.178121] RAX: ffffffffffffffda RBX: 0000000000000000 RCX: 00007fa8e97c48f7
[98340.178121] RDX: 000000000281f000 RSI: 0000000000000000 RDI: 0000000000000003
[98340.178122] RBP: 0000000000000003 R08: 0000000000000001 R09: 0000000000000400
[98340.178122] R10: 0000000000000018 R11: 0000000000000246 R12: 0000000000000000
[98340.178123] R13: 0000000000001000 R14: 0000000000000000 R15: 0000000000001000
[98340.178124] ---[ end trace 0f002bfb0ca96f0e ]---
[98340.178133] ------------[ cut here ]------------
[98340.178143] bdi-block not registered
[98340.178146] WARNING: CPU: 1 PID: 654183 at fs/fs-writeback.c:2321 __mark_inode_dirty+0x177/0x380
[98340.178146] Modules linked in: fuse snd_seq xt_nat veth nf_conntrack_netlink xfrm_user xfrm_algo xt_addrtype br_netfilter overlay ctr ccm xt_MASQUERADE xt_conntrack xt_CHECKSUM ipt_REJECT nf_reject_ipv4 xt_tcpudp nft_compat nft_chain_nat nf_nat nf_conntrack nf_defrag_ipv6 nf_defrag_ipv4 libcrc32c nft_counter tun bridge stp llc nf_tables nfnetlink binfmt_misc nls_ascii nls_cp437 vfat fat intel_rapl_msr hid_logitech_hidpp intel_rapl_common x86_pkg_temp_thermal intel_powerclamp coretemp kvm_intel joydev kvm irqbypass rtsx_usb_sdmmc mei_wdt mmc_core rtsx_usb_ms memstick iTCO_wdt iTCO_vendor_support watchdog wmi_bmof crct10dif_pclmul iwlmvm crc32_pclmul mac80211 ghash_clmulni_intel libarc4 snd_hda_codec_realtek intel_cstate intel_uncore snd_hda_codec_generic efi_pstore intel_rapl_perf ledtrig_audio iwlwifi snd_hda_codec_hdmi efivars pcspkr snd_hda_intel i2c_i801 snd_intel_dspcfg sr_mod snd_usb_audio uas cdrom snd_hda_codec snd_usbmidi_lib usb_storage snd_rawmidi cfg80211 snd_hda_core
[98340.178158] snd_seq_device mc snd_hwdep hid_logitech_dj rtsx_usb snd_pcm lpc_ich ehci_pci e1000e sg rfkill snd_timer ehci_hcd mei_me mfd_core ptp mei snd pps_core soundcore wmi button parport_pc ppdev lp parport efivarfs ip_tables x_tables autofs4 ext4 crc16 mbcache jbd2 crc32c_generic hid_generic usbhid hid sd_mod evdev i915 crc32c_intel ahci libahci aesni_intel libata i2c_algo_bit glue_helper drm_kms_helper crypto_simd cryptd xhci_pci scsi_mod xhci_hcd drm usbcore usb_common fan video
[98340.178166] CPU: 1 PID: 654183 Comm: sqlite3 Tainted: G W 5.5.0-2-amd64 #1 Debian 5.5.17-1
[98340.178166] Hardware name: Acer Aspire TC-603/Aspire TC-603, BIOS P11-B0 10/17/2014
[98340.178167] RIP: 0010:__mark_inode_dirty+0x177/0x380
[98340.178168] Code: 8f f0 ff ff 49 89 c4 48 8b 00 f6 40 5c 02 75 1c 49 8b 54 24 08 83 e2 01 75 12 48 8b 70 50 48 c7 c7 80 78 af 82 e8 cb 9d db ff <0f> 0b 48 8b 05 a0 bf d3 00 48 89 85 c8 00 00 00 45 85 ff 74 0e 48
[98340.178169] RSP: 0018:ffffaf96485abcb8 EFLAGS: 00010286
[98340.178169] RAX: 0000000000000000 RBX: 0000000000000001 RCX: 0000000000000007
[98340.178170] RDX: 0000000000000007 RSI: 0000000000000086 RDI: ffff8ca153299a40
[98340.178170] RBP: ffff8c9f4c763728 R08: 00000000000007ac R09: 0000000000000004
[98340.178171] R10: 0000000000000000 R11: 0000000000000001 R12: ffff8ca12545ec78
[98340.178171] R13: ffff8c9f4c7637b0 R14: 0000000000000000 R15: 0000000000000000
[98340.178172] FS: 00007fa8e969a740(0000) GS:ffff8ca153280000(0000) knlGS:0000000000000000
[98340.178173] CS: 0010 DS: 0000 ES: 0000 CR0: 0000000080050033
[98340.178173] CR2: 000055fc3b321360 CR3: 00000002b297e005 CR4: 00000000001606e0
[98340.178174] Call Trace:
[98340.178176] fat_update_time+0x58/0x80 [fat]
[98340.178177] touch_atime+0xbe/0xe0
[98340.178180] generic_file_read_iter+0xb5b/0xd00
[98340.178190] ? _cond_resched+0x15/0x30
[98340.178191] ? _cond_resched+0x15/0x30
[98340.178193] ? dput+0x32/0x2d0
[98340.178195] new_sync_read+0x12a/0x1c0
[98340.178197] vfs_read+0x9d/0x150
[98340.178198] ksys_pread64+0x65/0xa0
[98340.178200] do_syscall_64+0x52/0x180
[98340.178201] entry_SYSCALL_64_after_hwframe+0x44/0xa9
[98340.178202] RIP: 0033:0x7fa8e98a9786
[98340.178203] Code: 89 02 b8 ff ff ff ff eb c5 66 2e 0f 1f 84 00 00 00 00 00 90 49 89 ca 64 8b 04 25 18 00 00 00 85 c0 75 11 b8 11 00 00 00 0f 05 <48> 3d 00 f0 ff ff 77 5a c3 90 48 83 ec 28 48 89 54 24 10 48 89 74
[98340.178203] RSP: 002b:00007ffc7eb4ab38 EFLAGS: 00000246 ORIG_RAX: 0000000000000011
[98340.178204] RAX: ffffffffffffffda RBX: 0000000000000200 RCX: 00007fa8e98a9786
[98340.178205] RDX: 0000000000000008 RSI: 00007ffc7eb4aba0 RDI: 0000000000000004
[98340.178205] RBP: 0000000000000008 R08: 00007ffc7eb4ac18 R09: 0000000000000400
[98340.178206] R10: 0000000000000200 R11: 0000000000000246 R12: 00007ffc7eb4aba0
[98340.178206] R13: 0000000000000008 R14: 00007ffc7eb4aba0 R15: 000055ba64cd5930
[98340.178207] ---[ end trace 0f002bfb0ca96f0f ]---
[98340.178225] FAT-fs (sdd): unable to read inode block for updating (i_pos 449041)
[98340.178236] FAT-fs (sdd): unable to read inode block for updating (i_pos 449044)
[98340.273275] usb 1-4.3: new high-speed USB device number 14 using xhci_hcd
[98340.295205] usb 1-4.3: New USB device found, idVendor=2237, idProduct=4228, bcdDevice= 4.01
[98340.295208] usb 1-4.3: New USB device strings: Mfr=3, Product=4, SerialNumber=5
[98340.295210] usb 1-4.3: Product: eReader-4.21.15015
[98340.295212] usb 1-4.3: Manufacturer: Kobo
[98340.295214] usb 1-4.3: SerialNumber: N---redacted---
[98344.014041] FAT-fs (sdd): Directory bread(block 28064) failed
[98344.014048] FAT-fs (sdd): Directory bread(block 28065) failed
[98344.014052] FAT-fs (sdd): Directory bread(block 28066) failed
[98344.014055] FAT-fs (sdd): Directory bread(block 28067) failed
[98344.014059] FAT-fs (sdd): Directory bread(block 28068) failed
[98344.014062] FAT-fs (sdd): Directory bread(block 28069) failed
[98344.014065] FAT-fs (sdd): Directory bread(block 28070) failed
[98344.014069] FAT-fs (sdd): Directory bread(block 28071) failed
[98344.014085] FAT-fs (sdd): Directory bread(block 28064) failed
[98344.014089] FAT-fs (sdd): Directory bread(block 28065) failed
[98345.525698] usb 1-4.3: can't set config #1, error -110
Update: Most of the DB checksums in the recovered db are wrong...