So far the methods to transfer a game from the PC to PS3 have been:
1 - External HDD
2 - USB stick
3 - FTP server
For me none of these were an option for very large games for various reasons, so I tried transferring a game piece by piece and sure enough it seemed to have worked.
I'm not sure whether it needs to be done or not but but I kept the file required for the manager to recognize the game by name (I forget which, param.sfo? Someone please confirm...) on the USB stick I was using. Without keeping the file there the game would be recognized just by the code/root folder name.
Then I started up an FTP server just to make sure it overwrote the same file (for recognition) I kept and it seemed to have done so.
One thing I wanted to note is that discs copied through Open Manger to the HDD have their codes' letters and numbers separated by a dash (such as BCUS-98164) in the GAMEZ folder while the games available online to download all seem to have the code as one with no dash. What I'm getting at is one of the two is technically incorrect.
When copied from an online source it would display by the folder name which everyone makes without the dash. Meanwhile any associated game data are in the game folder (one directory up from the manager folder where the games are) does not use a dash either, and that's the official Sony directory rather than homebrew. I guess in conclusion I'm saying if it were even the folder of the game which was what was detected rather than the manager code Sony might still detect it as a copy based on whether or not it has a dash.