Hi
All I can advice is to see the dates of the last file modification on Your server and leave them on the server and overwrite everything else.
Or change the names of the last modyficated files and overwrite everything and than rename it like they should be watching the site. Unfortunately probably some files can be modyficated in both versions
ATTENTION UNIX USERS: Renamed files inside directories will be deleted while directory copy.
So the best would be to make a backup, copy new version and than copy the changed code watching the site changes.