I agree recently there have been a issue or 2 that messes up renewals . Actually you get warning your licence is expired or about to and you get stressed as you have 15 mths left. I assume this is not your issue correct?
The new account layout does not allow the user to remove PCs from the account. If you uninstall via windows and then run MCPR the removal tool the PC should dissapear but if the PC dies the PC stays on the account.
WE have been asking that the user have more rights in the account but if you want the account cleaned up contact support and get them to remove the extra PCs and get your extra licences refunded if that is what you want.
Supposedly the extra PCs disappear in 90 days but it appears the licence is still seen till then thus the warning that you are using too many licences.