Here is one solution. Add a clear button to manual entry system. Probably a good idea anyway. This allows the user to zero out a memorycard/precinct/countergroup combination. User then increases the number of memory cards in the vcenter, and counts only those precincts on the new card. We already that part.
I would like to hear suggestions on how this could be made more transparent though -- ie automatically clearing the recounted memorycard/precinct/countergroup. This still sounds far too easy to screw up.