I have folders synced between a few Ubuntu PCs and one Android phone. Some of my synced folders have bash scripts I use frequently, but they keep losing executable permission. I can chmod +x a file at the terminal and run the script fine, but a few seconds later its lost its permission again. My permission setting is only maintained if I kill the syncthing process. I have all my folders set to ignore permissions so I don’t know why it keeps changing my permissions.
Check at the change log in UI if there is any indication on where it’s coming from.
It’s possible that the file just keeps get changed by android for some reason, and the new file just uses umask that doesn’t have execute bit set.
Perhaps, if android supports it, you might want to enable permission syncing.