Are you just trying to freshen things up a little, eliminate some small glitches? If so, just re-install windows on top of itself to restore the system and operating files. All you have to do is insert the CD in your drive, go to Run, and type D:/setup to start the process, then follow the prompts. Afterwards, run defrag and regclean, and you are all set.
If you are using a new operating system now and want to get rid of win98, just go to add/remove programs and delete win 98. You won't lose anything, because all your data is duplicated in the folders of the new operating system.