Welcome to the community, @Wietse_Sennema1!
I don’t know of any programmatic way to do that, but probably the easiest way would be to duplicate your entire base (to become a new source base), and then start deleting tables from your previous base (which is now your destination base).
Then, for every table that you delete from your destination base, you can replace it with a synced table from your source base.
(And back in your source base, you would delete unnecessary tables as well.)
Maybe others will have other ideas for you, too!