How to get pagination to work with 2 wordpress loops

So you have a big problem here and a pack of small problems.

The big one is — pagination cannot be reliably changed within template. It just doesn’t work like that. Pagination and main query are processed before template is ever reached.

So I would guess information you are coming upon is about the need to properly adjust main query, rather than “combine” loops.

The pack of a small problems — how do you expect one page number to make sense for two completely unrelated queries? It’s like reading two different books at the same time.

You seem to be splitting post into virtual “kinds” of post via custom field. Why that have its uses, it wouldn’t be my first take on this issue.

Without knowing more details my first take would be to introduce Custom Post Type for anything other than native post and make use of its own archive for navigation.