Each Steam library on NTFS should have its own entirely new folder made for its compatdata on the Linux partition with the symbolic link being created to point to it, and absolutely should not use the default Steam library's compatdata or an existing compatdata folder from any other Steam library.
When attempting to use Steam to move a game between two libraries sharing the same compatdata folder, all of the game's files in compatdata will get deleted in the process because it doesn't know they are the same. Technically that could be fixed so it detects that and just leaves the files alone, but until then, the folders need to be separate.
In reference to the linked section of this wiki page: https://github.com/ValveSoftware/Proton/wiki/Using-a-NTFS-disk-with-Linux-and-Windows#preventing-ntfs-read-errors
Each Steam library on NTFS should have its own entirely new folder made for its compatdata on the Linux partition with the symbolic link being created to point to it, and absolutely should not use the default Steam library's compatdata or an existing compatdata folder from any other Steam library.
When attempting to use Steam to move a game between two libraries sharing the same compatdata folder, all of the game's files in compatdata will get deleted in the process because it doesn't know they are the same. Technically that could be fixed so it detects that and just leaves the files alone, but until then, the folders need to be separate.