Delete your game data, then use filezilla to copy the game over again, and select the "overwrite files if different size" option, then near the bottom check apply to this queue only.
This will let filezilla copy only the missing/corrupted files (if there are any). Do this 2-3 times and watch to see if it transfers any new files. I had a problem with the new blackbox FTP server on one of my games where it appeared to successfully transfer around 10 files but they never actually transferred, I had to switch to the old FTP app to get those remaining files to transfer over successfully.
Currently the FTP apps out there are not fully stable, so always make sure to copy it at least twice to make sure all the files actually transfer.
That's all the advice I can give for the moment. I have an internal 1TB WD drive, but I don't have a copy of uncharted 2 to test right now.