Provided you don't do anything else (like formating the disk) Gpart alone will only write out the partitions or "fencelines" around the disk. This data is stored in the partition table which is in the first sector of the disk. It does not write anything to the areas of the disk where data is stored, so it should not damage the data on the disk. The most that can go wrong is that it has guessed the "fencelines" wrongly, in which case, the data of one partition ends up in another. On the other hand, formating the partition will with something like Qtparted may well destroy the data.

The way I see it, you don't have much to lose, since you are going to reinstall XP on hda1 anyway, so you don't mind losing the Server2003 data on hda1, and the XP data on hda2 is going to be replaced by a fresh install on hda1.

But before you do it, read more about gpart. Here's a good link: http://www.stud.uni-hannover.de/user/76201/gpart/