I don't use aggregate often, so I just did this to check:
* created 2 test orders of the same recipient list upload product.
* aggregated the orders.
* after aggregating, the items land in from ready to produce queue, I processed all records and checked the output file (in ready for delivery queue). All good.
* I then pushed the orders back from ready for delivery to pending queue by using "resubmit" and then "revert".
* selected to process the orders using "prepare" and then "process one copy" this time instead of aggregate.
* checked the output file for both orders in ready for delivery queue. Again all good. Just the one copy of each recipient ready for the copies to be set on the press - same as I would have gotten if I did that in the first place.
I am not sure why you are having problems?