I'd say that you don't really need to differentiate, since the pre-merge records were references to the same document. After the merge, you only have one single record, and it belongs to all collections that contained one of the pre-merge records. So the resulting situation tells you that you found a reference to the document in both databases, which feels right to me.
Numbers: the number of items in each collection will only change if said collection actually contained 2 copies of the same reference. Otherwise, you have the merged item instead of whatever record was in there, i.e. no change in the number of items.