Sometimes it works out just fine and sometimes you end up with a buggy OS and end up formatting and doing a clean install. It can't hurt to try first. If your install of 98 is good now and you are concerned about having to formating and mess with something that is not broken, get yourself Norton Ghost and a second hard drive and image that baby in full.
This has saved me many times and when I want to mess, I can always go back.
LJ