Is there a special procedure I need to follow to get the ECU to relearn / figure out the proper settings after a battery disconnect?

I recently had an alternator go bad en-route, tried to make it to the shop but ran out about a mile out. By that time the battery was completely drained of course. Called up a friend, picked up a new alternator and got a jumpstart.

It's a dual fuel vehicle (gas and propane). Since that disconnect, when running on gas I feel a distinct hesitation when pushing the accelerator and a sightly uneven running and lack of power at speed. It runs fine on propane, which essentially bypasses the entire fuel control system.

Bram