The funny thing is that Windows deletes everything but your data folder for some people. The data folder holds all the actual files for the game and the files that Windows decides to remove are just your PSO2 executable along with some other files in the main directory.
If you had a friend who could just give you the executable and the remaining files that were deleted, you wouldn't need to redownload the whole 60 gigs.
Also, it's always good to make a backup of your game so you don't have to keep re-dling the files.
Also in doubt install Arks-Layer Tweaker.