Steps to reproduce:
1) Define new or edit and save existing maven 2/3 build job which uses alternate settings.xml file
2) Have Jenkins run that job (this step at finish clears configured alternate settings.xml of the project)
3) Every next build fails - editing build job shows that alternate settings.xml is cleared

Following commit is likely cause: https://github.com/jenkinsci/jenkins/commit/a254f202f971497a277f758cae5de84292073a4d so bug is there since 1.426