I have the following scenario:
Now,
Unfortunately it looks like your pull-request will remain an orphan.
See this (still unresolved) thread: https://github.com/isaacs/github/issues/168
Probably the best thing to do would be to re-clone the repo, re-create your pull-request, delete the existing pull-request, and submit a fresh one.
Also, add a "thumbs up" to tohe issue so in the future there can be a more straight-forward solution to this problem.