Note that there’s no need to move the tables, just exclude those documents from the Scrivenings session.
Just as a general best practice, in most situations you probably don’t want to load hundreds of files into Scrivenings mode anyway. You certainly can, but navigation will be easier and performance will be better if you only load the specific chunk you’re working on. A few chapters rather than an entire novel, for instance. The whole point of Scrivener’s design is that you don’t need to deal with hundreds of pages in a single enormous document.