With the blue ocean creation wizard, it replaces the GithuSCMNavigator each time when there is a new pipeline added (with the new pattern). the side effect is any tweaks to branch settings are reset to the defaults (eg for building pull requests, or not...).
What should happen: should only change the pattern, no other settings.
this is addressed by https://github.com/jenkinsci/blueocean-plugin/pull/1188 - which can be completed when the new branch source stuff is released.
This also may be made redundant if we migrate away from org folders (I think 1188 is still warranted though)