Normally XP should produce a warning if you attempt to merge any *.reg file with something like "Are you want to add this information..."
Offhand I can think of a few potential solutions...
1) Run XP's Restore Tool from Start-->All Programs-->Accessories-->System Tools-->System Restore and choose a date immediately prior to your registry merging. With any luck this should set your system back to its pre-PDA modification, and save you the trouble of either manually fixing all the keys yourself and/or reinstalling XP.
2) If that fails, and you have the reg file from your PDA, you could edit the pda reg file you saved on your desktop by right-clicking on the reg file and selecting "Edit". It should then safely open the reg file in notepad, and you can see which keys were modified and change the corresponding Win XP key via regedit. That could potentially be a very tedious task depending on how many keys got changed.
3) If 1 fails, and 2 is too daunting, you could restore from a
backup (*.bkf) file, if you created one, or you could manually restore the registry via this
method.
Good luck!