On Arch Linux, FreeFileSync version 6.15, I just found that, when syncing and writing the files to EncFS, the timestamp is not preserved. As a result, the modification time of the is based on the time the file is written. This produces the problem to sync the file next time.
If the file is copied to the EncFS directory without using FreeFileSync, but a file browser, the timestamp is preserved.
This problem does not appeared to ext4.
EncFS modification time problem
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Thank you @Zenju, the problem solved with [404, Invalid URL: https://freefilesync.org/FreeFileSync_6.15_bugfix_Source.zip]see viewtopic.php?t=1701Zenju