If a ref disappears, it's job will become disabled, however any running builds of this job will not be aborted. This can result in the build trying to checkout code from a deleted ref which, most likely, will result in a failure. This becomes an issue when the failure of a build gets reported back to a code review system eg Gerrit.

It seems logical that an orphaned job should also have any builds aborted as they cannot succeed and will result in an incorrect failure case.