When running the multibranchPipelineJob step it seems like it overrides the sources of a Multibranch Pipeline Job instead of just updating it. After running the step, even though nothing has changed the output of the branch indexing will become:

Checking branch master
      ‘Jenkinsfile’ found
Met criteria
Takeover for job-dsl-plugin_multibranch » master by source #1 from source that no longer exists
Branch reopened: master (b409f3996299dd12244d6cf7f8b6d8df3aa674ca)
Scheduled build for branch: master

To test this, I have installed a brand new Jenkins with the Pipeline plugins and Job DSL plugin (all as the stable version) and made a freestyle job, with a Job DSL step that has the following script:

multibranchPipelineJob('job-dsl-plugin_multibranch') {
  branchSources {
    git { 
      remote('https://github.com/jenkinsci/job-dsl-plugin.git')
    }
  }
}

After running the Job DSL step and afterwards running branch indexing a "master" job is created with the following log message from branch indexing:

Checking branch master
      ‘Jenkinsfile’ found
Met criteria
Scheduled build for branch: master

When running branch indexing again, following log message are shown as expected:

Checking branch master
      ‘Jenkinsfile’ found
Met criteria
No changes detected: master (still at b409f3996299dd12244d6cf7f8b6d8df3aa674ca)

However, if I run the Job DSL again and run branch indexing, the first log message (with takeover and so on) are shown. This is not what I would have expected, I would have expected something like a "no changes detected" message.