You don't describe your problem very well, but I doubt if reinstalling Windows 98 will help solving disk errors. I would advice to buy a new hard disk and copy everything from the old one to the new one. That might very well help.
If you want to stick to the old one, find a boot diskette (and be sure it works!), then format c:. This will surely stop scandisk from running automatically, because it just isn't there anymore. if the format finds bad sectors (seems likely to me) buy a new hard disk. Same goes if scandisk with surface check gives errors now. But you've lost the information on the old one then.
Hope this helps.
Need to disable Scandisk in order to reinstall Windows. Scandisk is caught in a loop and Windows 98 will not boot up in either Normal or Safe mode. Can only get into DOS. Tried to run Chkdsk...won't run. Scandisk takes foreer and found some bad sectors on HD but HD diagnostics said there were no errors. Want to reinstall WIN 98 from CAB files but Scandisk keeps interferring so I want to disable it until I get Windows installed. Any ideas? Thanks.