Duplicate folder structure on new computer

The migration tool I used to move to a new computer did not handle Adobe Element as expected and I failed to double check until had made some changes to the pictures folders.  I now have a good backup of the catalog from the old computer and need to restore it to the new computer but I'd like to keep the changes I already made to the picture folders.  Any ideas for how to best do this and not have duplicate folder structures or duplicates in the catalog?

Thanks for your help!