Fox's analysis of the Bat

If I'm remembering right, the techs say that the change was 'checked in'. I took this to mean 'checked into source control'.
That is:

• There are two bats
• They both use the same software, which includes (non-functional) autopiloting.
• Bruce Wayne was planning on using one of them, but needed the autopilot fixed. So he modified the autopilot. Being the nice guy he is (or perhaps just not wanting to lose his work), he checks his changes into source control.
• During a regular maintenance cycle (perhaps when the techs booted up the second machine), the software is pulled and deployed to the other bat.
• The existence of a working autopilot is communicated to Lucius Fox.

Descriptions of the bomb in the movie are inconsistent, but at one point it's mentioned that it's a neutron bomb. A neutron bomb would have a higher radiation yield but less destructive power. There's a good analysis of the bomb's potential effects here.

Therefore, though it would be hazardous to salvage at ground zero, it's plausible that the aircraft could have been found intact.

The whole ending is up for interpretation and how Lucius retrieves the Bat seems to be part of it. When he first shows Bruce the Bat it is a prototype, and he tells Bruce "and yes it does come in black." This suggests to me there is more than one. The black one Bruce uses, the one we see the techs in at the end is the original prototype first shown to Bruce. As someone said, when Bruce fixes the autopilot on his black Bat, maybe it synchs with the prototype. The techs said it was fixed 6 months ago. So the autopilot is working long before Bruce takes the Bat out across the bay. The confusing thing is why he tells Selina there is no autopilot. Perhaps just to throw her off to enhance his planned fake death, not to mention just a way of tricking the audience.

There was never a single bat. The armory had more than one and we can see that Bane uses them for city patrol. When the techs check the other bat, we see that it has been patched in the auto-pilot issue. But the thing is, Bruce Wayne wouldn't have a favorite Bat and use it every night. Being realistic, it's quite possible, damages occur and that he keeps switching between them, Hence he needs the auto-pilot fixed on all of them. And I don't think he was planning on using it to destroy the bomb. It was fixed six months ago, like the tech says. It was a spur-of-the-moment thing when Bruce saw his out and decided to take it. He saw Blake stand up to the bad guys and that's when he gave the co-ordinates of the cave to him. Then he just lies to Gordon ( or Catwoman ) about the auto-pilot and takes his way out of the crime-fighting business.

As for the bomb explosion being huge, so what? He just got off way ahead near the bay. They never did show the last few seconds ticking and Batman's face together. He had enough time (close to 40 seconds). And the speed with which Bat travels, say 250 m/s ( it's a futuristic plane, it could even be supersonic but we never saw the sonic-boom ), so 40 seconds counts for 10 km. Now that's pretty safe and far off.

I too had this doubt and just realised this: the bat shown in the film ending is not black in colour...so it should have probably been synced with the other one