Home is in the flood zone. It secures loan A and its equity is partial security for loan B. To determine the amount of flood insurance do we have to add both loan balances together and then compare that figure to the RCV?

yes

So, even though loan B has other security, we still have to use the entire loan balance in our calculation, correct?

When it comes to calculating flood insurance coverage other security, regardless what it is (unless it's another structure requiring flood insurance), has absolutely no factor in determining the amount of required insurance.