Synchronize Folder problem - LR finds missing photos that aren't missing

A bit of background:
I decided to dive in and clean up a big 40K catalog I have. This involved:
Moving images around
Creating new folders
Renaming existing folders
Renaming all photos
All of this was done within LR to avoid problems. But now, everything is working fine, LR does not complain that there are missing photos EXCEPT when I try to synchronize a folder.
The strange this is there is no question mark on the images and when I use the Find Missing Photos, LR tells me that there are no missing photos.
But when I try to synchronize a folder (any), it finds all the images as new images and suggests to remove the missing photos (both matching the exact number of images). Obviously I don't want to do that and loose my edits...
I found some information here, it seems to be an old bug but no solutions work for me... I really don't want to go back and redo all this work. Is there a magic trick?
Thanks!

Thanks but this a completely different problem. You are referring to the "Treat JPEG files next to RAW files as separated photos" setting that I have unchecked purposely and I do not shoot RAW + Jpeg anyways.
Your issue is a normal behavior. LR assumes that Jpeg+RAW shooters will only required the RAW to be imported in LR unless you change that setting.
My problem was a very specific instance where the volume name did not match case with the folder names in LR. As soon as I fixed that, it went back to normal.

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