As far as I know, Boot Camp is completely compatible with NTFS-formatted partitions, and should not cause you any problems booting or uninstalling Windows XP.
It is worth noting that if you're using Mac OS X's mount feature to transfer data to and from the FAT32 partition, once you convert it to NTFS, Mac OS X will only be able to read from the partition. There's software available for Windows XP that can read and write to the HFS+ (OS X) partition, so that might be of interest to you if this is an issue.
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