We have noticed that either the github-organization-folder or workflow-multibranch plugin sometimes redefines jobs completely, losing the build history for the repo/branch jobs that were deleted or overwritten. The first time we noticed this, was during a GitHub outage. It has happend more often though, and we have not figured out a pattern yet.
Anyone any idea? Maybe a pointer to the source code where this issue might be at? Then I can have a look for myself as well (I'm not a Jenkins expert).