My game got stuck loading the gateway ship for an infinite time, so I had to task manager the game to close it, this resulted in the C:\Program Files\ModifiableWindowsApps\pso2_bin folder going corrupt.
Add or remove programs > Repair
Says app data will not be affected, but when it's finished, when you run the launcher, you need to wait for the patch to download again, takes as long as your internet takes to download it.
Hopefully it doesn't happen a lot, I see above a lot of people have had the issue multiple times, so sorry to hear that, having to download the game again once is painful enough.