Tried uninstall/reinstall version 5.5 and 5.7
It's only happing with a few folders
Tried new Catalog
When I reimport them it dims the file like a duplicate until I tell it to allow duplicates.
Lightroom show the files in the Archive folders, I think this is the issue.
I think I got it, it was poorly documented feature.
When Importing, you are given the option to create another copy of the raw file as a backup.
I recently did the online update to 5.7 and it did an uninstall of 5.5 then installed 5.7 rather than just append the updated files.
During this it must have updated the catalog with the backup/archive folder. Once it did I could no longer see my CR2 file where they should have been.
To fully resolve this I'm going to have to move the archive a location outside of the pictures folder and reimport the missing folders.
Sync did not work for me.. I suggest to all is to ensure your backup/archive is not in the pictures folder.