There is a script provided in the install "<install_location>\SDD_HOME\standard\examples\pcb\Automation\Scripts" called DeleteDuplicateVias.vbs.
You can drag and drop this file into Xpedition and it will remove the duplicates.
I tried the script you mentioned. It resulted with 0 duplicated via.
Therefore, either extra holes are related to test points or they come with the
I double checked both of them and I got removal of most of my wished test
points and no change in the duplicate files
It looks I need to look somewhere else