You can try to add field to your tables to store a "database"specific key made of a concatenation of the database name\number and the autonumber.
So for PK 1 to 10 in DB1 you would have DB1_1,DB_2,.....DB_10. Once you merge the dbs into one you now have a wy to relate back to the original ids and you can run update queries to update the FKs with the new autonumber PKs.
I used to do a lot of this kind of stuff and I found out the best way to do it was to create a "script" made of "numbered" queries (a thing I came up with
). I would name my queries 001_APPEND_ImportTable1_DB1,002_APPEND_ImportTable 2_DB1, 003_UPDATE_Table2DB1_FKs,.... I have a form that had two textboxes for start \end query number and a button to run them. This way I could run the script and modify it multiple times until I got it right.
Cheers,
Vlad