Best way to fix broken links to catalog clone?

I keep my LR Catalog on an ext HDD. I also clone that HDD for backup. I recently went on a trip with the Clone HDD and used it as my main drive. When I got home I just cloned it back to the other drive and figured I was set.

The drive that "was" the main user drive, now says it cannot find images. If I select an X image and locate and make sure it is "finding nearby images" it works, but not the whole drive, there are still thousands of images marked missing. The paths to both drives is the same "except" on drive is called "clone", which I have to do in order to make sure I am using the right drives when I backup. Hope that makes sense.

Question is: "What is the best way to get this drive properly in sync with the catalog AND is there a better way to make sure this doesnt happen again?

Thanks

Henry