[Nook Color Q&A, Help & Troubleshooting] jaromrnelson:
Update 20111117: Updated .zip file to Adobe Flash 11.1 and AIR 3.1.

Update 20111020: Updated .zip file to reinstall Flash and AIR, previous version didn't properly fix AIR.

Steps I used to update Adobe Flash (to version 11.0) and AIR (version 3.0) so it doesn't update automatically and thus get me back into the boot loop cycle (again):

Go to Titanium Backup ( Pro :) )

You need to uninstall with this since these are system apps

Buy a Pro key and keep it on your SD card root, since this app will save your bacon :)

Uninstall Adobe AIR and Adobe Flash Player from Titanium Backup

It will warn you that you are uninstalling a system app, that's OK

I think that is why the update through Market isn't working

Open Market, Install Adobe Air (3.1.0.488 as of this post) and Adobe Flash Player (version 11.1 11.1.102.59 as of this post)

Nook seems to be working after several reboots. Also, note that Adobe updated their apps. After following the procedure above, I was able to update via Market without any problems with bootlooping.

Obviously, the above steps only work BEFORE Adobe gets auto-updated and you get in the boot loop cycle. If you are already in the boot loop cycle, download this file (Updated link, should work better this time):

FlashPlayer11.1_AIR3.1_Update_Fix_20111117

and install it using a ClockworkMod Recovery SD card.

Get a ClockworkMod Recovery SD card

http://xdaforums.com/showthread.php?p=11987469

Put the zip from the above post on the SD card

Reboot your Nook with the SD card inserted

Install from Zip, Select zip from SD card, select the flash update

This basically will uninstall flash and air as system apps and install as a user apps. This is based on the zip from GMPOWER which updated flash to 10.3, which worked for some but not others, perhaps because it didn't touch Air:

http://xdaforums.com/showpost.php?p=16526691&postcount=7

Also note, I have been through several cycles of restoring backups, restoring to factory, re-rooting, etc. this last week, so I was getting very annoyed and cautious. I think I was able narrow it down to just the Adobe updates causing my problems. I have been able to update ROM Manager, Superuser, and just about everything else with updates; and besides the Adobe updates, everthing worked, and I don't currently have a boot loop problem.

Note, I didn't update Superuser or ROM Manager until after I applied the above updates to Flash and AIR. After several reboots, my Nook is still working fine.

For those of you who are still having trouble getting your Nook back, and the attached zip doesn't work for you, you can do the following. Using the instructions on this site, I got my Nook back up and running to factory new condition:

http://mrm3.net/nook-color-recover-any-bricked-device/

(Quick method at top, not older methods below; instructions slimmed down from several posts here at XDA, updated for stock 1.2) also here on XDA:

http://xdaforums.com/showthread.php?t=914690 (original restore to stock post)

http://xdaforums.com/showthread.php?t=1050520 (update for stock rom 1.2)

Then, I registered my Nook (again).

At this point, I could have tried to update to 1.3, but my patience was a bit low, so I didn't go for it. If you do, be sure to follow the appropriate ManualNooter instructions here:

http://xdaforums.com/showthread.php?t=1054027

Since I was still on Stock 1.2, I rooted using ManualNooter 4.6.16

(while in CMR, after running ManualNooter, I also applied update-Froyo1.2-dalingrin-OC-emmc-090111.zip, and that seemed to work without a hitch)

Then I reinstalled all the other apps I wanted on my Nook,

=== BUT DID NOT YET UPDATE ADOBE FLASH OR AIR ===

Flashed ClockworkMod Recovery, updated a lot of my apps using Market and Amazon Appstore, restored data and other apps from Titanium Backup,

Then I made a full backup of my Nook using CMR. (still booting normal, running fast and clean)

After confirming my Nook was as I wanted it, and that I had a good backup, I did the steps at the top of this post to update Adobe Flash and AIR.

After confirming that was working, and getting another backup on my SD. I then did the updates to ROM Manager and Superuser. It seemed like those updates happened at the same time as the boot loop, so I was cautious. My Nook is still working well without boot loops as of yet.

Results:

Kernel: Stock 1.2

Rooted with: ManualNooter 4.6.16

Additional Mods:

update-Froyo1.2-dalingrin-OC-emmc-090111.zip,

ClockworkMod Recovery 3.2.0.1,

ROM Manager 4.5.0.1, Titanium Backup 4.5.2,

Adobe Flash 11.1, Adobe AIR 3.1 (uninstalled system app, reinstalled via Market, updated via Market)