Richard,
Esri is aware of this issue. As you've observed, it seems to be an issue with the latest fnp toolkit. Our team is currently working with Flexera to address the issue. We have a bug logged in our SalesForce tracking system. If you like, please contact our Technical Support and asked to be added to the list of customer experiencing this bug, BUG-000123662. In doing so, you can monitor the progress of the bug.
As for the bug itself, it affects both ArcGIS Desktop and ArcGIS Pro Concurrent licenses. Even though the Availability displayed less than the actual licenses available, all licenses are still available for use. In your case, your users should be able to check out more than 5 Pro Advanced licenses, up to 25. This is only a display issue and should not affect the users.
If this is urgent in your environment and cannot wait for the fix, again contact Technical Support and ask to have all your licenses combined to a single entitlement. This will only work if your licenses have the same expiration date such as yours.