I've encountered this situation myself. I normally list on .ca but somehow during a week a while back I discovered I had listed several items on .com. Of course someone purchased 2 items and when I tried to combine, it didn't work.
I went to online help and talked to someone there, who asked for the item numbers of the sold items. He very knowledgably confirmed that yes, one item was listed on .CA and one item was listed on .COM....haha....not alot of help there.
I ended up just discounting the shipping on one of the items and sending out 2 separate invoices which wasn't very convenient but was the only option I seemed to have.
Joy