Well, Gaylen, I'm no IIS expert ... in fact, I spent all Friday afternoon trying to get IIS re-installed myself (it had stopped working because of a lot of Java junk that got loaded and re-loaded on my system last year by a co-worker ... he got his stuff semi-working, but IIS has not been the same since).
I ended up un-installing it and it did not seem to lose my virtual directories at all, because once I *finally* got it re-installed, there was no problem with the virtual directories. They remained intact. I would suggest making a backup of them all, just in case, but it worked fine for me ... (disclaimer ... YMMV <g>)
Maybe someone with a bit more experience will give their 2 cents.
~~Bonnie