WIN XP boot problem

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this is my hard disk condition right now.
one physical hard drive with two partitions..

C:/ had win 98 files and main boot files. it is the primary drive. i recentlf converted it form fat 32 to ntfs making WIN 98 not work.. i was unaware it does not work in NTFS.. so i deleted the WIN 98 folder, program files folder and windows folder on this drive.

D:/ is still a fat32 partition and has my WIN XP and is a logistical drive(says acrosis disk director)

is it safe to leave it in this condition or do i have to shift my boot files from C: drive to d: drive??

i do not wish to format any drive
 
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