There's been reports of SEGA's launcher deleting system files (and oddly enough, some FFXIV files) if the following are true:
1. You installed PSO2 into a different directory/drive than the default one.
2. You downloaded the precede files.
3. You ran SEGA's patcher (while it was working) and had it finish the entire update for you.
Ugh, SEGA.
Images:
PSO2launcher.exe checking and attempting to delete FFXIV files:
A screenshot posted by someone on 2ch showing his/her registry with missing files, deleted by SEGA's patcher: