Ok so Im just sharing this in case anyone else runs into this.
Shortest possible summary: I had an old dongle for a legacy version of Cubase, I had a newer dongle for the new version of Cubase. For reasons that arent clear the new licenses for the UR44 plugins were placed on the old dongle (eventhough I purchased the UR44 after purchasing Cubase 9 and had not used those plugins in anything BUT Cubase 9). Then the old dongle DIED. This explains why it was a sudden issue, why ONLY those plugins were affected, etc etc etc. Also why there were changes in the licenses shown in the eLicenser.
So I implemented Steinbergs Zero Downtime and it all worked like it was supposed to. If you end up with a defective dongle not all hope is lost. They deactivated the old dongle and gave me new activation codes for the things on the old dongle. Yay.