Hi Martin,
I re-read your question and I might have misunderstood your problem, sorry about that.
I thought that you had agents in updating state, but I'm now realising that instead it's the Fleet Server state that it's stuck in "updating" state in the UI. Is it correct?
Of course in this case disregards my previous response, since it would unenroll your existing agents.
Would you mind to share some screenshots of what you see?
Thanks,
Cristina