No, that is not the current version, so get the new one please. This won't fix the issue.
As I understand it, you had another product running , or the items were copied in there from a destination, right?
The toolbox is 250 if you are not on Premier Support, and if you are, it is half price. With Premier Support you can get us to fix this for you and it would take about 30 mins or so and have plenty of time to command our attention moving forward. It is 4 hours, never expire until you use it for only 399. There is another option, you CAN do this by yourself, for free, but it is not the best option in my opinion.
You can export the contacts to CSV, and then reimport to a local empty folder, stripping any copy flags, and then copy to the existing (emptied) source folder, but you would have to make sure to set all the relationships to remove destination copies if source items are deleted to avoid duplication. Your relationships are probably set that way already. I prefer to do in place stripping because it avoids the potential for data loss, like pictures or attachments and is cleaner.