Hi Homer,
It sounds like the license being compatible and not expired it accumulated the two totals between the different license (as each being a separate license it combined the available on the two and this is how the number doubled). It is not expected that the application of a new license will invalidate the old license, and only the removal or expiration of the original license will invalidate those seat allocations.
I would suggest the following:
This document: http://eyeontesting.com/questions/5511/how-to-remove-a-license-from-qcalm-v115x.html . convers the removal of licences. I would suggest removing al licenses on the system following the procedure and then adding back in only the new license.
In this post it states to remove You can remove the data from the following qcsiteadmin database/schema tables, then restart the ALM and DB services:
DELETE from td.LOGIN_SESSIONS
DELETE from td.SESSION_LICENSE
DELETE from td.SITE_LICENSES
We used same method of upgrading in our development environment and we did not have this problem, so we have nowhere to test this but in production.
This should set the available seats to the correct amount you have legally purchased.
Hope this helps,
Dan