The Fleet Points are not being handled correctly if France is conquered (i.e. Marseilles taken on same turn as Paris). The rules state that one French Fleet point is sunk while the second becomes a British Fleet Point. Rule 9.522
So, you need three possibilities for the software:
1. Both French FP in the Atlantic, then add one FP to British Atlantic Fleet and both French FP disappear.
2. Both French FP in the Mediterranean, then add one FP to British Mediterranean Fleet and both French FP disappear.
3. One French FP in each of the Atlantic and Mediterranean, then Pop Up to let player decide to which Sea Zone he wishes to assign a new British FP and both French FP disappear.