There is an issue with the bitbucket multibranch scanning if bitbucket goes away during the scan as this is not detected as an error case and instead the branches/jobs are considered as no longer existing and are therefore deleted (and new jobs triggered on the next scan when bitbucket server is back).

It seems that the multibranch scanning works in two "phases".
First phase is to find all the branches, if bitbucket is already offline during that time, everything is fine as it will just fail the scanning and not update any jobs.

The problem is if bitucket is online during that time. So it finds out all the branches. Now in the second phase, each branch is checked for the Jenkinsfile. Now if during that phase bitbucket is offline, it's not resulting in an error, it's instead resulting in a "Jenkinsfile" not found which will then delete that job.