.var folder is not synced

[0146754]

The .var/app folder in the user directory contains Flatpak data, FFS only sees its own directory (I installed it as Flatpak) and all the others folders for the other apps are ignored (they are not excluded) and when mirrored against a populated .var folder all the folders excluding FFS's one are deleted.

[xCSxXenon]

This sounds more of the OS limiting the scope that apps can see, and 'sandboxing' them

[Zenju]

Third-party builds of FFS are not supported.

I'd suggest testing if the problem reproduces with the official FFS version: https://freefilesync.org/download.php