Perhaps I misunderstood your situation.
In your first post you said "i recently bought a new pc and began to delete some file on my old one running 98"
By that I assumed you have two pc's the new one with windows xp and the old one with windows 98
Is this correct ?
Since you deleted some of the files in your old pc you probably deleted some of the files needed by the operating system
The boot disk was for the windows 98 pc so you can get some of your files from there

Now you are saying you want to format your pc that has xp with windows 98 ?
Are you sure you want to do that ?
Is there any reason why you wnat to do that ?