You should be able to start the game without Epic Launcher detecting it. I haven't tried it with GTA but other games from Epic can be started from .exe files directly from the install folder. I have Metro and Witcher 3 games installed a long time ago and they do not appear in EGL because I moved game files to another drive, but I can play those games.
If #1 ...
Depends where you have it installed.
Let's say you have 2 drives/partitions C: and D:
Windows is installed on C: and GTA on D:
If you format C: and reinstall Windows you won't loose any files on D: and GTA should work fine.
If you only have one drive and one partition then you could make a backup of the files on an external drive.