What’s the main issue? Is the error actually causing you operation issues with you licences?
E.g. if your allocations where completely broken you could clear the licence
files and re-allocate, the licence allocation information is stored in .pgo
files on the server (installation and root folder configured in the QVMC).
You could stop the QlikView services, back up and clear the files and bring
the services back online (which replaces the files blank). I've fixed odd
licence issues before like this usually caused in older version via corrupt
files so it's pretty much equivalent of turning it off and on again.
This issue could be with the Qlikview Directory Service. If you haven't tried restarting that service yet, just restarting it may work.
The Service may show as running but could be having some issues.
Please see this link also: