When I syncronize a folder, LR wants to remove AND import ALL photos and place them in a identical folder folder at the top of the hirachy and leave the “original” folder empty.
I had a similar behavior some time ago. In my case the sync of the parent folder was somehow corrupted. As a first step I did a fresh sync/import of my „root“ folder for Lightroom, which resulted in a duplicate folder hierarchy within the Lightroom. And as a second step I removed the „old“ folders from my Lightroom catalog. Since then everything works fine again.
I am having the same exact issue right now. I am reading through the thread, was there anyone that knows why this happens? I currently tried to re-sync a folder and its asking the same. To remove all photos and re-sync them again and it will add them into a duplicate volume in Library mode. So weird, but I'm getting very frustrated with it.