I had a similar issue, two identical websites sharing several models but with different objects. Unfortunately, merging them by natural_key was impossible.

I had to implement a new django commands similar to loaddata, in order to append all models from the second website into the first one.

You can find the code of the solution in this gist:

https://gist.github.com/MattFanto/f6c0ee0bc392da1d0d90f28efdb77e40

there's always the dump data from django, which is pretty easy to use.

or you could do this manually:

• if the 2 databases share the same data (they are mirror one to another) and the same table structure, you could just run a syncdb from django to create the new table structure and then dump and import (i'm assuming you're using mysql, but the general idea is the same) the old database into the new one
• if the two databases share different data (still with the same structure) you should import every single row of the two databases: this way, you'll keep relations etc, but you'll have your unique id updated to the new sole db.
• if the two databases are different in both data and structure, you'll have to run two sincdb and two imports, but this doesn't seem to be your case