Thanks for reaching out via Twitter. It’s still a pretty puzzling issue. It sounds like both databases are synchronizing somehow. Here’s what I’d suggest:
- Make a backup of both sites (I’d suggest manually saving website files and exporting a copy of the database via phpMyAdmin).
- Disable the backup plugin you used (both sites).
- Try updating the menu on your primary site to point to the correct URL for one of your menu items. You mentioned seeing a 404, but I was able to access the main site using the correct URL.
- If the menu stays the same on your development site, you’ll know it’s the plugin that was causing the issue.
If the menu changes on your development site, then there’s still something else linking them. At that point I’d suggest trying to change the database password for your primary site (support can help with that) to see if that breaks the connection. You can test if it did by using the same method described above.
Once you figure out how to disconnect the databases, you can then work on updating the current site to change all your URLs back. There are tutorials online that explain how you can do this using plugins or phpMyAdmin to make the process faster. Hope that helps. ^Jesse