Cloned Build Plan stuck on default repository

I created a Build Project that involved the use of 5 shared repositories. Then, I cloned this project, and changed the default source repository, to have branches automatically created and built when changes occurred on this second repository. When I manually run a branch (Gatekeeper turned on w/out push), I get a build error, and the log tab has the following:

Checked out: develop 31179....
Merged with: feature/feature1 c4c284....
Failure reason: Merge command error: fatal: 'c4c284....' does not point to a commit

The interesting thing is that the develop hash is the same as the develop HEAD for the repository that was the OLD default, evidence of it looking at the wrong source repository. Even if I change the default, the cloned plan doesn't work. However, when I rebuild the plan from scratch, it works as expected.