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.