How to merge two databases (each with different updates) on the same server
(Disclaimer: I'm not familiar with WordPress and I haven't used phpmyadmin very much.)

If there is new data in each database since the "split", i.e. each database has some unique new data not found in the other one, then I don't think there is an easy path for merging them just using standard MySQL commands or tools. There will be records in one database with the same primary key values as in the other database, but with different data in the other columns in those records. If there aren't a lot of such records, then you may be able to merge this "manually", record by record, but it will likely be labour intensive and you need to know what you're doing. E.g. when you give a record a new primary key value to avoid a collision with the other database, you also need to make sure to update every foreign key that refers to it.

That said, there are special WordPress plugins for exporting and importing WP databases, and I'd be surprised if these didn't allow you to merge two databases. See e.g. wp-exporter and wordpress-importer. But that is probably outside of the scope for this site. See also this question on stackoverflow: How do I merge two Wordpress SQL databases in phpmyadmin?