Hi, If you re-install Win98 over-top of itself, you should not have any problems. What will happen, is that the installation will replace any 'system' files. You will keep all of your current settings, device drivers, programs, user preferences, etc. It will use the current 'registry'.
If there are any errors or problems with the registry, it will not correct those. A re-install on top of the current Win98, will simply replace the dll's and system files with ones from the CAB files forthe installation. If you have applied any security patches or critical updates, these may be over-written. In this case, you would need to re-apply the patch, or update.
An install on-top of a current installation is usually a 'safe' thing to do. This may correct the problem you are having. However, if it does not correct your problem, you can still always do a clean re-install. But this will be done after you have installed over the current Windows 98 installation.