Here is a simple description how to reproduce the bug:
Create a text file on an FTP server (Shift+F4 in remote folder), type "abc" into it and save it. It uploads. Then change its contents to "12345" and save it. Open it once again and chances are you are going to find: "abc45" (instead of "12345").
It's the same while updating files during synchronization (in both directions). File update works well if the new file is of the same size or smaller than the old one but not when it is larger. I tried to find a workaround but found none.