This seen this in the read me..
3.4.6 Resupply in patrol
The resupply feature in mid ocean is not available for this installment.
This issue will be addressed in further patches.
You should always pay attention to your diesel fuel and try to avoid remaining out of fuel in mid ocean, and you can opt to refuel at forward bases.
But never seen anything about if I used this option.
Is like SH3 as in your mission and renown scrubbed if you resupply?