How does one remove unused W98 from secondary disk on XP system?

[tjs]

Have 1999 Micron PC (now P-III-550), originally with W98 and 13GB drive single partition:

-  Added a 60GB drive to use as XP Pro boot disk / primary drive after partitioning in roughly thirds.  XP is SP2 updated.

-  No other OS partitions, but allowed cable swap of drives to move back to W98 during the "migration" (60GB would not be seen).  Original 13GB is now second disk. 

-  Did not remove W98 then but have never used it since (too unreliable)

-  Added different graphics card and replaced CD-RW later so W98 will not likely boot. 

-  Have a recent full back up of the second disk

-  Down to a few meg space on all partitions

-  Looking for ways to get rid of the W98 system files from original drive without losing any of the original app support files that might have been put under "windows". 

-  Prefer to not wipe 13GB then move most everything back over. 

This isn't a classic uninstall to me, but may be it is though W98 isn't "running".

Any ideas?

[patio]

Not clear on what you want to accomplish so i'll ask a few questions...

Is the XP drive the main HDD?
What do you mean when you say you need some system files from Win98 ?
Do you switch cables to boot to the Win98 drive ?
Anything on the Win98 drive has nothing to do with XP running properly so i would just format the whole drive and be done with it.

Personal data from there though should be backed up first...

There's no reason to move XP over to the 13G drive...use it for storage instead.

[tjs]

Clarifications:

Per bullets 1 and  3, XP is on 60 GB HD and is active system.

Per bullet 7 I don't need W98 system files, just files that apps may have put in the windows area (if any).

Per bullet 3 I do not boot to W98, and because of hardware changes I doubt that I could if tried.

I know XP doesn't use W98 files and I could format 13GB (bullet 8 ) but I do not know which apps will be orphaned by restore of all but W98 system  file areas from full back up.

13GB already stated as secondary (bullet 2).  As indicated in bullet 6, I am low on space and want the W98 files I no longer use to be gone.

Anyone else have any ideas or advice on utilities?

[patio]

That's alot of bullets...i'm still unclear on why you are worried about losing anything from that drive...
If it's a program it would need to be re-installed under XP anyways...
If there is data such as documents or photos just back them up and wipe the drive...

[tjs]

When I installed XP on the 60GB, I do NOT recall reinstalling anything that was on the 13GB drive.  I just had both drives connected and installed XP on the60GB and the apps that I have on the 13GB worked just fine. 

I installed office 2002 for students to get Word 2002 on  60GB.  Apps on 13GB include AOL, MS-works, and Word 97.   Each Word runs independently, each with a different license string.  other apps are there too, so they must be looking at the 13GB drive for data.