in theory when you recover then you don't lose any files, all it does is restore defaults (so yes restore back the registry keys), but your personal files should remain, if on the other hand you do a custom install that would delete all files on computer and make it like new. To get all the programs that came with your laptop go to the acer website and and you should find it there, otherwise if you remember which programs you had install, there is a large probability that you can just google them and download.
if you repair, the main problem that i can foresee is that there would be an error which says that some part is unrepairable, which would mean that you would need to reinstall windows, other than that i cannot say for with any certainty what the problems could be.