You can download old versions of full Zotero releases, but I don't believe all versions of Zotero beta (which 5.9.97x was) are archived, no.

Zotfile works with 6.0. Mdnotes simply hasn't been updated. It'd likely work with 6.0 after a simple fix (but also note that Zotero has md note export in the beta now).

You can downgrade your database by reverting to the pre-beta automatic back-up and then syncing (make sure you're fully synced before downgrading and keep a back-up of your data folder).
https://www.zotero.org/support/zotero_data#restoring_from_the_last_automatic_backup