There are a couple of different programmers that would be on your bike.
1) Add on
2) ECM Reprogrammer
Neither should lose a tune if you disconnect the battery
If you have the add-on, it should be plugged into the 'ECM' which is attached above the battery. These add hardware onto your bike.
If you have the ECM reprogrammer, it would have come with the bike. They are 'married' to the ECM, and can't be re-used. These just re-program the factory ECM, the nice thing is that you don't need to have additional hardware on your bike, that can stop working, and then your bike would then die, or go back to stock tune, which could be really bad IF you have a cam in the bike.
Most bikes out there would most likely have a 'HD' tune, or a tune that is downloaded from the dealership. These are usually very LEAN and run hot.
Anyway, hope this helps!