Hey Barry,
That is very interesting!
Just to provide some insight as to the inner-workings of License Manager and the Laserfiche Server, License Manager delegates licenses to users and then the Laserfiche Server enforces that you must have a license to sign in. License Manager and Laserfiche Server must be in sync for proper functionality. When operating normally, the Server will periodically poll License Manager for the updated list of users. All this information is logged in the Named User database, so ultimately, if you're getting the error you listed, it's ultimately because the Named User database didn't list the user as being valid or having a license.
It's possible that the poll hadn't happened yet after the Server restart, but not polling isn't a reason for the Named User Database would get modified. Since Laserfiche Server is the component enforcing licenses that are delegated through License Manager, then the Named User Database shouldn't have been modified yet and you shouldn't have gotten the error that the user didn't have a license.
Was there any work done to the Named User database during the restart?
In the future, make sure that you leave enough time after the Laserfiche Server comes back online for the poll to take place (or change the polling interval through License Manager). Additionally, you should verify that the Named User database remains unmodified during the restart.