PrimusThe3rd When you move to archive, this function deals with the duplicates. Like if same file is already where you try to put it, it will be deleted instead. So it is normal that some of the photos will end up in the trash. However, if you have your doubts, I would suggest you to do some random checks - like take some of file names and look for them in the Tonfotos to make sure those are indeed duplicates.
However, this is assuming those files were put there by Tonfotos. Can it be that they ended up in the trash bin some time earlier?