Well, I was sure that I had no duplicates in the first place. So I knew that any duplicates would be false-positives.
Basically, if you want to merge two histories together, it's always best to export whatever you have in the target history, empty it completely and then import everything you need to import into it.
That way, there will never be any duplicates.
For example if you have history A from 10th till 20th, then history B from 4th till 12th which is from a DIFFERENT SOURCE, then you can import history B into history A without checking duplicates and all will be fine.
However, if you export history A and you would import that export into history A again, you would get all of the messages duplicated (if you turn off the duplicity check).
Basically... it's best to export history A always prior to importing, and then empty history A and import everything.
I dunno it sounds complicated but that's how I did it, and I got like 4 years of histories imported with no problems.