You should be ok - and the nag message will drop off after 90-days. You can continue to use the product, and functionality will not be affected.
We are having the same issue. Support claims this is the reason our scans are getting errors. They also said it's the reason some scans do not show a vulnerability report, only a network assets report. Has anyone else experienced this?
Going over your license count should not produce any errors. Can post a snippet of the log file and the error.