Here are two possibilities. In either case start by backing up both files using different names that includes the current date. (Cautious should be my middle name!)
1. Export both files as gedcoms, create a new PAF file (with a new name) and import both gedcom files. Do an automatic merge based on Unique record serial identifiers. When you are finished that, do an automatic merge based on AFNs, which may pick up a few more duplicates. Lastly do a very careful manual merge based on exact spelling. When merging, if in doubt, DON'T!
2. Buy FamilyInsight from ohanasoftware.com and use the "Compare and Synch" function to move people from the SMALLER database into thr larger one.