For this same reason i had two separate folders with FFXIV pre Dawntrailer because i had some bad files that didn't let me play cutscenes from ARR without crashing the game (Example: every Praetorium cutscene would close the game) and if i clicked the restore file thing in the launcher it would redownload the whole game deleting all the contents from one of the folders. My final solution yesterday was to delete all previous installations of the game and download the 98Gb from DT and make a second copy of the game just in case something like that happens again.