I have reproduced this on SAB and RAB 10.1. This worked fine on 9.2.4 for both App Builders.
When I rename a project (Language Bible) to (lng-Language Bible), some of the project subfolders go to the new project folder name, and some stay in the old project folder name. After that point the project is understandably very erratic. Recombining the manually does not fix the issues.
Reverting back to RAB 9.4.2 corrected the issue.