stevenatcisco: I don't think the directory is required for the replay operation. If I delete the @libs workspace on the master by hand, replay still work fine. There is a copy of the required files of the library in the directory of all builds. I am guessing this one is utilized for what ever the replay requires it for, or the required commit is just checked out from the repository again.
No matter, there is still a @libs directory in the directory for the master workspaces, that just sits there forever. It contains the in my case implicitly loaded shared libraries for each job. And there are a lot of them due to heavy use of feature branches and pull requests. It can't be deleted by the pipeline and it's not automatically deleted if the associated job in Jenkins is deleted. Also I do not have any build processors enabled on the master node, so that workaround with switching to the problematic directory directly does not fly as well, because I can't get into the master workspaces with the pipelines as far as I know.
The one way to get rid of those directories I was able to come up with is to have the server run a nightly cron job that clears our the workspace directory of the master, so the issue does not get out of hand. That solution works, but I'd rather solve that issue inside of Jenkins.