When upgrading Notes Migrator 4.0 from a trial license to a real license, trial licenses (due to trial migrations) do not get reset with the new key. The number of licenses remains the same.
This behaviour is by design. However, there are ways to resolve this and get the correct number of licenses.
1. If the users from the trial license are live users that will be migrated in production (same source address) then migrating them with the production key will not count a second time.
2. The approved method for resetting the license count would be to make a copy of the Default Settings (File > Edit Default Settings, aka the old INI file), delete the NME database, recreate the database, configure the default settings and then paste the old "INI" file over the new "INI" file. This way all the settings are back in place and the license count is reset.