You also say that you switched from USB to eSATA. There is a very good chance that from the perspective of the OS these are entirely new dives, maybe even seen

You also say that you switched from USB to eSATA. There is a very good chance that from the perspective of the OS these are entirely new dives, maybe even seen as internal drives. There may not be an issue in the Time Machine code, but rather this whole thing is unfortunate edge case of intended behavior.