They seem to be on different servers because the registrar has moved the domain to some kind of holding server thingy. They’ve always been on the Amazon web hosting in Germany. The current .org server also has the .com certificate. The only way .com can be on another server is that the registrar is redirecting the domain to their own servers. The main site is on the Germany server.
The main problem is however, how do I remove the .com certificate and replace it with a .org certificate? I keep getting the errors given above no matter what I try to do.