I make every effort to keep the correct metadata in my LR catalog. After import it is not important to me what metadata is stored in the original image file copy except that it at least contains the metadata delivered with the file created by the camera. When I export, I create a new derivative image file and it will always contain the metadata that I choose to export from the catalog file. Because of this and because the original image file copy and the catalog can so easily get out of sync for the reasons that Jim mentioned as well as flags set by the system backup software, I simply ignore any differences between the metadata stored in the catalog (my gold standard) and the metadata stored in the original image file copy.
I always ignore the LR metadata warning alerts.
On the Export dialog there is a Metadata section with a "Include" dropdown that gives several options to be omitted or included. Below that are 3 checkboxes that should be self explanatory.Clee01l, What do you mean by: "When I export, I create a new derivative image file and it will always contain the metadata that I choose to export from the catalog file."? And how do you do this?