Did you remove the folder ProjRep out of the project folder you were copying too?
During our upgrade we used the new dbid created on ALM 11.52 and changed the PROJECT_UID to the number of the old project and changed the PR_SMART_REPOSITORY_ENABLED to N. We then removed the folder ProjRep from the newly created project and copied the old data in the new folder. It then allowed us to add the project, repair and upgrade.