Yes I did enable it. I figured out that it was causing the the problem but it would be great if there was some sort of warning that some transactions were not uploaded due to the unique reference.
The holistic approach here would be to use an attribute that actually is unique across all relevant systems. With that being easier said than done, you can create a new queue and configure it so it does not require unique IDs.
Another option is to loop through the previous reference IDs as new items are added - if an equal reference is found then bounce that item back with a suitable error message.
Without knowing the reason why the issue with unique IDs appear it is hard to come up with a tangible solution.