Uninstalling Win98 on WinXP

[Nischint]

Volumes converted from FAT to NTFS lack some performance benefits compared to volumes initially formatted with NTFS. On converted volumes, the MFT might become fragmented. In addition, on converted boot volumes, NTFS permissions are not applied after the volume is converted

That's what the XP Support had to say. Now my French isn't what it used to be, but does this mean that converting only one drive will get my comp messed up?? In addition to this, there's nothing mentioned about data loss. So I'm assuming that I will lose some data.

All this seems extremely complicated. And to think it started out with me wanting to just uninstall Win98 on one partition

What if I just delete the folders and files that are Win98 specific, and then remove the entry from the dual boot? Will it work?

Added later:

What's better? Converting a FAT32 into NTFS, or formatting it directly into NTFS?