Yeah, your yyp files stay wherever they are. If you do a completely fresh reinstall as per the instructions, they will no longer show up in recent projects, though, so you'll have to find them wherever you saved them
Given the fact you're asking this question: Please look into version control software! make an account at github.com and store your projects there. Easy to do refactoring / testing, reverting to backups (as well as keeping an off-site backup), and checking back changes that you made.