The new e2fsck 1.43.4 (31-Jan-2017) has definitely helped, but I'm still seeing some flakiness with inline_data directories. There's still a kernel problem, which is creating file systems that confuse e2fsck. But I have more data on the e2fsck problem which is mis-correcting that problem so it takes a second run to get a clean file system. Specifically, e2fsck is creating the missing system.date problem on one run and then zeroing out the directory on another. The problem is occurring when I rsync to a small directory. Consider the following directories: 1461410 (12) . 1421827 (12) .. 1461583 (20) potd-800.jpg 1472133 (36) .xvpics 1461401 (72) .potd-800.jpg.4176 1461314 (12) . 1421827 (12) .. 1461426 (20) potd-800.jpg 1463943 (36) .xvpics 1461400 (72) .potd-800.jpg.4176 During the rsync run, I got syslog complaints: [255031.626936] EXT4-fs warning (device md3): ext4_dirent_csum_verify:352: inode #1461410: comm find: No space for directory leaf checksum. Please run e2fsck -D. [255031.626940] EXT4-fs error (device md3): ext4_readdir:198: inode #1461410: comm find: path $PATH1: directory fails checksum at offset 0 [255035.720542] EXT4-fs warning (device md3): ext4_dirent_csum_verify:352: inode #1461314: comm find: No space for directory leaf checksum. Please run e2fsck -D. [255035.720547] EXT4-fs error (device md3): ext4_readdir:198: inode #1461314: comm find: path $PATH2: directory fails checksum at offset 0 The inline data consists of two parts: 60 bytes in the block pointers which hold the first four entries, and 72 bytes in an ea, which holds the fifth and last entry. debugfs on the directories reveals the following: Inode: 1461410 Type: directory Mode: 0755 Flags: 0x10000000 Generation: 927521379 Version: 0x00000000:00000007 User: 1000 Group: 11 Project: 0 Size: 132 File ACL: 1496481792 Directory ACL: 0 Links: 3 Blockcount: 8 Fragment: Address: 0 Number: 0 Size: 0 ctime: 0x5902fa22:07728174 -- Fri Apr 28 04:15:30 2017 atime: 0x5902fa22:07728174 -- Fri Apr 28 04:15:30 2017 mtime: 0x55016b84:e7729ec8 -- Thu Mar 12 06:33:40 2015 crtime: 0x56c1c093:0d01b4b4 -- Mon Feb 15 07:12:03 2016 Size of extra inode fields: 32 Extended attributes: system.data (72) Inode checksum: 0x456bd90c Size of inline data: 132 Inode: 1461314 Type: directory Mode: 0755 Flags: 0x10000000 Generation: 927521364 Version: 0x00000000:00000004 User: 1000 Group: 11 Project: 0 Size: 132 File ACL: 1496383488 Directory ACL: 0 Links: 3 Blockcount: 8 Fragment: Address: 0 Number: 0 Size: 0 ctime: 0x5902fa22:07728174 -- Fri Apr 28 04:15:30 2017 atime: 0x5902fa22:07728174 -- Fri Apr 28 04:15:30 2017 mtime: 0x55016b84:1670325c -- Thu Mar 12 06:33:40 2015 crtime: 0x56c1c093:01161e74 -- Mon Feb 15 07:12:03 2016 Size of extra inode fields: 32 Extended attributes: system.data (72) Inode checksum: 0x008d7abf Size of inline data: 132 If I run e2fsck on that stat, it complains about two things: Inode 1461314, i_blocks is 8, should be 0. Fix<y>? yes Inode 1461410, i_blocks is 8, should be 0. Fix<y>? yes i_file_acl for inode 1461314 ($PATH2) is 1496383488, should be zero. Clear<y>? yes i_file_acl for inode 1461410 ($PATH1) is 1496481792, should be zero. Clear<y>? yes I don't really understand how those two errors were created in the first place. However, after saying yes to those, the system.data ea is missing and the final entries in each directory get dropped, leading to being dumped in loat+found. Here's the state after the first e2fsck run completes: Inode: 1461410 Type: directory Mode: 0755 Flags: 0x10000000 Generation: 927521379 Version: 0x00000000:00000007 User: 1000 Group: 11 Project: 0 Size: 132 File ACL: 0 Directory ACL: 0 Links: 3 Blockcount: 0 Fragment: Address: 0 Number: 0 Size: 0 ctime: 0x5902fa22:07728174 -- Fri Apr 28 04:15:30 2017 atime: 0x5902fa22:07728174 -- Fri Apr 28 04:15:30 2017 mtime: 0x55016b84:e7729ec8 -- Thu Mar 12 06:33:40 2015 crtime: 0x56c1c093:0d01b4b4 -- Mon Feb 15 07:12:03 2016 Size of extra inode fields: 32 Inode checksum: 0xcd34b98c Size of inline data: 60 Inode: 1461314 Type: directory Mode: 0755 Flags: 0x10000000 Generation: 927521364 Version: 0x00000000:00000004 User: 1000 Group: 11 Project: 0 Size: 132 File ACL: 0 Directory ACL: 0 Links: 3 Blockcount: 0 Fragment: Address: 0 Number: 0 Size: 0 ctime: 0x5902fa22:07728174 -- Fri Apr 28 04:15:30 2017 atime: 0x5902fa22:07728174 -- Fri Apr 28 04:15:30 2017 mtime: 0x55016b84:1670325c -- Thu Mar 12 06:33:40 2015 crtime: 0x56c1c093:01161e74 -- Mon Feb 15 07:12:03 2016 Size of extra inode fields: 32 Inode checksum: 0x042ed119 Size of inline data: 60 This then leads to a second run complaining about Inode 1461314 has INLINE_DATA_FL flag but extended attribute not found. Truncate<y>? If I instead fix it by "ea_set -f /dev/null <1461314> system.data", I get the directory back in a relatively unbroken state. But why is system.data being deleted in the first place?