ECU Firmware Update from Ford?

So, I have a 2007 Mustang 4.0L V6, that has an FRPP CAI with a tune from Bama Tuning... It's been having some trouble over the summer with the AC/Heat fan going out. I had put a new relay in thinking this would fix my problem, and so it did -- for awhile.

It had went out again quite some time later, about the time I was heading back to school. So I took it into a shop as I wouldn't have time to look at it. They got into it, and decided it was the BCM (Body Control Module) that was shorting out. Now, while they were calibrating the BCM to coordinate with my key remotes, they decided to "update" my ECU with a new firmware from Ford addressing a few recall issues? Now, the car, at this point, would start up and chug quite vigorously and throw several lean codes. Understandable as I'm sure this new firmware overwrote my tune, and is now not used to the increased air flow.

So, the shop got back to me tonight, and told me that they contacted the CAI manufacturer (FRPP I'm assuming) about the problem, and they were told it would need an entirely new air intake setup because of this firmware, and that I should send it in and exchange it for a new one.

My question is simply this: I have the Bama tuner SCT SF3/X3 with three tunes relative to the mods currently installed on the car. Can I just re-marry my tuner with the "stock" file on the car, and re-flash my 93 octane tune? I'm hoping I can backup the stock file from the tuner to my HDD, wipe the stock file from the tuner completely, and re-capture the stock from the ECU; allowing me to re-calibrate the engine. As it stands I cannot even flash the ECU which leads me to believe I have some marriage issues between the ECU and the tuner.

Note: This is just the information I've been able to gather from the shop as of this afternoon, so you know as much about it as I do at this point. I don't have the slightest clue as to why they would even touch the ECU as it wasn't having any issues, but they decided to update it anyway. *FACEPALM* I'm just trying to gather some viable information so when I get access to it tomorrow afternoon I can hopefully make it a quick fix.

Thanks for your time!