Joe, it’s often dodgy to look at someone’s database entries when they report issues as they may have edited and removed some entries by the time they post. What you see is often the result of lots of “finger prodding”.
As Guru says, the new database uploads will enter activator, S2S and chaser QSOs in one pass. This works fine until someone notices they have made an error. If this was an error in the activation records, then the normal action was to delete the activation, fix the file and reupload. Now that the file contains S2S and chaser QSOs, you will get warnings that there are duplicates. The real fix in this case is to delete all the QSOs that were uploaded.
There are several solutions to the problem and all have different levels of messiness to them. One would be when you reload an activation and the S2S and chases are spotted as duplicates, you could have check boxes that say “only upload activation” or “only upload S2S”. Another way is to note which QSOs were uploaded at the same time and then have a “delete everything upload in upload #12345” and let the database clean up so you can reupload.
For now, if when you retry, you get things marked as a duplicate, either delete them because they are in the file you are trying to reupload. Or delete them from the file and upload.