I solved this issue, it was my error, the Asobo's default OMDB was still installed. If you have this issue, follow these steps:
in MSFS Content Manager, search for OMDB
in the search result, you see a line for Premium Upgrade
to the right of Premium Upgrade, there is a blue 'list' icon, click it to expand all the content inside Premium Upgrade
in the expanded list, find OMDB and uninstall it
Now all duplicate artifacts/POI are gone.