I am not able to reproduce the behavior you describe but suggest that you don't modify the XML Export. The XML Export has ID's that uniquely identify objects. If you just change e.g. the name of a referenced PI Point, you will not succeed. I assume duplicate objects might be due to your modifications to the XML Export.
I suggest you to use PI Builder add-in for Microsoft Excel if you like to apply bulk modifications.
You don't understand my problem:
I'm working on PI Coresight. My colleague is working on PI AF.
1) He exported his AF database in DB_V1.xml (contains <AFDatabase> <Name>DBTEST</Name>...)
2) I imported the xml file in a DBTEST I have created in PI System Explorer.
3) My colleague did modifications in PI AF so he exported the database in DB_V2.xml
4) I deleted and re-created my DBTEST database and imported DB_V2.xml -> all the elements appear twice!
Please accept my apologies. I would be able to ask now for installed versions but believe one of the next logical steps should be to reproduce the issue with the XML Exports that you get from your colleague.
Because I expect those files will contains sensitive information and also because the kind of issue you describe is better handled in Technical Support, I suggest you reach out to Technical Support.
Another thing of interest, likely also one of the first questions you will get from Technical Support, will be for the Options checked with the XML Export.