OK, I think I have found an answer to my own question. It appears that the broken admin pages with too many items were a result of my hosting provider (Dreamhost) having “extra web security” checked in the setup of the site. This apparently stops WordPress from updating when the query is too large. Disabling this “feature” restored functioning to this very large group of variations. It is slow, but thankfully, it does work and does update, even with 500 (and counting) variations. Hope this helps someone else who may be experiencing the same problem I was!
