The deletion of a build/run in Jenkins is handled by the delete() method.

It throws an exception, when the build directory on disk has already been removed and stops deleting the build.

Unfortunately, the hudson.tasks.LogRotator.perform(Job<?, ?>) method does not check for this exception and will STOP cleaning up, once even just one build throws that exception.

This behaviour can be fixed in the following ways (a pull-request will be uploaded shortly):

1. The Run.delete() method must still unlink the job, even if the build directory has been removed externally.
2. The log output of Run.delete() must be made less verbose (it prints the ENTIRE folder content by default, into the job that is doing the cleanup)
3. The LogRotator.perform() method must handle the exceptions being thrown by delete() gracefully.