I would backup my project and then run check with all of the options in the Project box checked except "Streamline Research Text Fields" and "Add Birth/Death Events". Do not check any options in the other boxes.
This should find the duplicate records.
Select the duplicate records and renumber them to some high number above the highest number in your data.
Do this again and again (if necessary) to be sure you have no more duplicates.
When you run check without finding any more duplicates, run check again only this time use the Repair option.
This should clean up any problems in the data and then you can renumber the high numbers to a low number and let UFT find an unused number to assign.