I have changed batteries in fobs and bikes and never had to reset them. I would also recheck the battery wire ends and make sure your getting a good connection.

 

You don't need to worry about resetting the key fob, there is no need.
What was the initial history of the bike not starting that made you get a new battery? Not being ridden or something else?
It sounds like you have a battery drain issue if it's going flat enough to not start the bike within 24 hours.
What is the make of the new battery and does it display the cold cranking amps on the side of the case. It will likely say something like 300cca.
If you have a test meter, what is the actual battery voltage after that 24 hours where it seems to lose voltage?

Some simple things to try without going too technical if it is a drain issue.
Are there any new powered accessories on the bike since the problem started?
Make sure the fuse and relay box is clean and not suffering from corrosion. Pull the fuses out and check.
Remember that there are two ends to the battery cables, both must be secure, not nipped up, but tight, and clean. The earth goes to the top of the transmission and a bit of a a pain to access. If checking the positive lead on the starter motor, make sure you disconnect the negative cable first or sparks may fly.
Recharge the battery then disconnect the voltage regulator and see if the problem stops.
If that doesn't work, recharge the battery again and remove the system relay which is located in the fuse box. If unsure which is the system relay, pull them both out. There was occasions when the system relay, either from corroded connections or a fault in the relay was cycling the Idle Air Control motor with the ignition off and draining the battery.
If that doesn't work, you can try removing one fuse at a time to see if a particular circuit is draining the battery.


You'd be best off initially doing some simple checks with a multimeter set to DC volts. Although ideally you want the negative test lead on the battery negative post, this is not an easy option so any solid earthing point should be okay.
Recharge the battery and leave it to settle for an hour. check the voltage across the battery. what is it showing?
Put the battery on the bike and turn the ignition and kill switch on. What is the voltage?
Press the start button whilst observing the voltage. How low did it drop?
When the bike is running, observe the voltage at idle and at approx 2000 rpm. What readings do you get?

Then turn the bike off and periodically check the voltage across the battery over the 24 hours.

Depending on your knowledge with multimeters, you can try doing a milliamp draw test if none of the above starts pointing you in the right direction to solving your issue.

Good luck.

 

Great information in the post above.
Personally I believe it to be your ground, because your battery appears to have had plenty of juice at 12.75 volts when it arrived at advanced auto for its progress report. This is totally negated if Advanced Auto charged your battery before testing. (Normal Practice)

Follow the advice from j_bee.
I know from past experience, riding a carbed 883 I could ride 45 miles on a fully charged battery, but yours has a fuel pump and Fuel injection.
Totally different animal.

Do the testing above and report back your findings..
The more information, the better the diagnosis.

The 1200 is a LOT of fun and a lot smoother than the 1000 ever was.