I'm also having this same issue on 5.7 on Mac.
It's not LR it is OS X.
That is unless you or the OS somehow changed those images since they were imported originally. And when I say changed I'm not talking about using the LR Develop module.
I'm on Windows and don't have any problems using the syncing folder option. Only new images I have placed in folders show up.
Well, synchronising folders works just fine in Capture One Pro 8 for Mac.
OS X and Windows have a different foundations so it's coded differently in LR for Mac than it is in LR for Windows. Plus, when I execute a 'Find all missing photos' command from the Library menu, LR says no files are missing - simply because they aren't. It's a bug in the synchronise folder module alright. And it's in LR.
I was able recreate same issue as you are describing at least for the below conditions:
"Find missing photos" shows no missing photos in the catalog.
Ran a folder sync test:
Results show that there are 0 new photos and will remove 7 missing (incorrect)
The missing photos are present in the catalog/folder, however I noticed these 'missing' photos are all JPGs with a DNG pair.
Changed the LR preference "Treat JPEG files next to raw as separate photos" so that it is checked
Repeated the sync folder test for same folder, this time it shows no missing photos and the new photo count is now 3 new (which is correct)
I had imported many DNG/JPGs as treating them as separate files before the Nikon D750 NEF files were supported.
After the NEF files were supported I switched preference back to not treating the files as separate files.
So some folders in the catalog there are file pairs present while the majority of the catalog is just NEF files in each folder.
Tested some other folders containing no DNG/JPEG pairs and they do not have a sync issue.
Does this help for your situation?
Thanks, bhousto90, for your work on this. Alas, it is not the solution. I've got the same problem in folders only containing RAW files. Checking the 'treat jpeg files..." option doesn't do anything.
It seems however we've narrowed it down (there are a few people in the other thread I've mention above with the same problem) to this behaviour occurring when the files and folders reside on another drive than the one the catalog is on. I myself have my catalog on my primary drive (an SSD) and all my images on a secondary hard disk drive. When I synch a folder on my SSD everything works as it should; when I synch a folder on my secondary drive the problem occurs and LR wants to delete all images in the catalog (including virtual copies and all edits) before re-importing them. Others that replied in the other thread have the same problem with networked or external drives.
I do hope Adobe picks this up.
I had exactly the same issue. So I started using Aperture again in the mean time as I was not going to lose my edits...
Today after I installed Lightroom CC and found out that the problem was there as well, I started to think about this issue. And I finally remembered that it happened once before. And I also remembered that it was something to do with a directory name being different on the hard drive as to what it was in Lightroom. So I started analyzing my library and hard drive.
I found out that on the top level directory in Lightroom library, the first letter of the directory name had somehow been capitalized. I have no idea how that happened...
So I renamed the directory in Lightroom - and voila! The problem disappeared!