You know, fonts are a funny subject.
First of all putting fonts in any other folder out side of your home folder is asking for trouble. You shouldn't be adding fonts to
Library/Fonts or
System/Library/Fonts (nor should you really be removing any from these places either).
The best place for fonts is in
~/Library/Fonts or in any other folder within your home folder (if you are using something like Suitcase or Font Book).
On the subject of
What happens when I reinstall?, that depends on what type of reinstallation you are planning on.
If you
Erase and Install... yes, your fonts are going to be gone (along with anything else you had on the volume).
If you
Archive and Install... there is a good chance that fonts outside of your home folder will be spared (if you are having the installer save settings and the like) and anything inside your home folder will absolutely be untouched.
So
offbeat, really none of us knows what is going to happen to your fonts because you haven't told us what type of reinstallation you are planning on. Plus we have no idea how you've been managing your fonts (where you've been installing them on your system).