As I understand it (and feel free to correct me if I'm talking a horrendous amount of horsesh|t), Avalaunch uses a database to store what the long filenames are and they're stored on the HDD similarly to DOS filenames (like 'BLAHBLAHBLAHBLAHBLAHB~1.XBE' - I didn't check character length on that example!).
So if you go back to EvoX, 95% of the filenames would be regular (any Xbox games can't by definition use illegal characters/long filenames) and ones that have had to be shortened would show up as the example above.
Put simply, you may have some shortened filenames if you've uploaded Goodrenamed ROMsets or DivXs or whatever but they will still work, they'll just be named differently to how they are on yr PC HDD.
Hope that made some sort of sense!