It sounds like the system files got corrupted but they are intact enough that it still detects the system when you download a new config so all it sends is the new config. If you could get it to also download the system files like it does when there's a firmware update it may clear it up but I'm not sure how you could force it to do that.

One idea though - are you using CCP? If so, maybe try downloading a blank config using the basic MX-980 Editor instead. It may not recognize the state of the remote and might force a full download of the system files as well. Assuming that brings it back to life you should be able to once again download the proper config using CCP.