I am a Level 5 ASC contributor and lord and behold, I have been having the same issue since the fall of 2014 when iOS 8.x was first released. I am going to explain the problem in detail and also the steps that have been taken to try to resolve, all to no avail.
Like the OP I had no issues with iOS 7. Starting in late 2014 and with every single iOS update since, the folders I have synced from my computer to my iPad get duplicated during the iOS update process. To explain, before an update I have Camera Roll, Recently Deleted, and 2 folders containing photos that I have synced from my computer via iTunes to my iPad (let's call them albums A and B). Immediately after an iOS update I end up with Camera Roll, Recently Deleted (both unchanged), the original albums A & B (generally unchanged), and extra/junk copies of albums A & B containing random photos from A & B. Sometimes I get one extra of each album, sometimes several extras. This has happened with every single iOS update since the fall of 2014. Once these junk albums appear they cannot be deleted from the iPad directly as they are coded as synced albums. The junk albums contain pointers (not actual photos) and the only way to delete them is to first delete the iPod Photo Cache on the computer, then doing a sync with no photos selected (this clears all photos except Camera Roll), then doing a new sync with albums A & B. The Photos App remains well after that until the next iOS update when the issue reappears without fail. So with every single iOS update in the last 18 months, after updating iOS I have had to clear all synced photos and then re-sync the ones I want. The extra junk albums show up regardless of whether the update is done over the air or through iTunes and regardless of whether I have one album or more than one. If I have one album only, it gets duplicated, sometimes once, sometimes multiple times but it is always duplicated after each iOS update.
I first contacted AppleCare about this issue in December 2014 and have had an open case with them ever since. I have spoken with a highly experienced Level 2 tech more times than I can count and the issue has been escalated to Engineering on several occasions, all to no avail. To summarize past steps, my iPad has been restored several times, both from backup and also as new to make sure no corruption was being restored back. All Apps have been re-downloaded and settings re-configured from scratch. My iPad was replaced by AppleCare to eliminate the possibility of a hardware issue. Potential metadata issues were suspected so I downloaded a 3rd party program to my computer and stripped the photos in question of all metadata. No metadata remains in these photos. I have synced different photos. I have replaced my main computer (original W7, new one W10). I have a fresh install of iTunes (12.3.3). None of the photos are 3rd party, i.e., they were all taken by me with a selection of cameras and there is no discernible pattern as to why they are duplicated. I also should point out that I keep a different synced album on my iPhone and the same issue has occurred there. It is not as repeatable as with the iPad. During some updates the album on the iPhone is left untouched but with other iOS updates the same duplication issue occurs (same photos, no change in album content).
This thread is one of several I have encountered in the ASC describing this issue and at this point I have two options, to live with the issue and re-sync photos following every single iOS update (what I have been doing) or delete all synced photos from the iPad permanently.
I will be emailing AppleCare again and linking this thread.
