It looks like some critter names are missing in the critter proto editor in WE, though they are in the in FODLG.MSG. No idea why, but the result is in the generated _npc_pids some of the names are NPC_PID_Unknown*, which makes scripts which used proper defines to complain.
If you didn't change critter names in the first 524 protos, then I think you can just take them from the original _npc_pids that we released, and replace the unknown ones WE generated for you.