Shoot, I should have read to the end. I searched PDF and a specific subcollection that had large PDFs, had to choose "includeP&C" to get anything to show up, selected all and trusted that even though everything was selected only the PDFs would go, and lost everything. I didn't see the warning about second conditions until too late.

But it's entirely my fault, and fortunately there were only about 30 items in the subcollection and I should be able to recreate it. Maybe the ability to filter by PDF size (either for searching above, or syncing below) would be helpful for some.