This looks like JENKINS-41214, but in a different environment.

I have configured bitbucket branch source plugin with a hg repository.
Then I have configured the job to add a Jenkinsfile library, stored in a git repository.

When building the job, I got an error "Changeset not found". It looks like the changeset is seeked in the bad repository.

My workaround was to disable the "sendNotifications" call of the onCheckout handler. (see attached diff)

Two "onCheckout" calls are triggered : one for my hg repo, and another one for the git library of my jenkinsfile lib.