When in Github Enterprise I create a new Pull Request from master to a branch (base: branch, compare: master) in Jenkins, master branch gets removed (master) and is not built anymore. This is kind of strange and rather inappropriate behaviour. 

Why to do PR from master to branch - this can be useful for review purposes on Github. Though as we are using Continuous Delivery from master, this is unacceptable for master to be removed. Strange thing is that as far as I have checked it breaks only when master is a compared branch one.