One report and one update request:

After collecting some information again for PR1.3, I was astonished upgrading to PR1.3 and patching openmode worked so flawlessly using the Flashing guide and the first post of this thread.

• Backup: Among preserving my data I made an internal backup, which was saved to MyDocs/.backups/Backup4 which I copied to my PC
• I downloaded the PR1.3 firmware using NaviFirmEx under wine, in my case important:
  • The rootfs (fiasco) image:
    DFL61_HARMATTAN_40.2012.21-3_PR_LEGACY_001-OEM1-958_ARM.bin
  • The EMMC image:
    DFL61_HARMATTAN_40.2012.13-7.ALPS_EMMC_ALPS.bin
• Downloaded the patched kernel http://maemo.cloud-7.de/HARM/N9/1.3/...dfl61-20121301
• Reset to get rid of BigScaryWarning: First went back to normal mode by doing a "Comprehensive Reset" using the images:
  
  Code:

  sudo flasher -f -F DFL61_HARMATTAN_40.2012.21-3_PR_LEGACY_001-OEM1-958_ARM.bin -F DFL61_HARMATTAN_40.2012.13-7.ALPS_EMMC_ALPS.bin

• Getting rid of the BigScaryWarning: Booted the N9 and installed developer mode and executed the command
  
  Code:

  disclaimer-cal remove View-openmode

  as advertised in this thread.
• The Nitdroid-thread here: forum.nitdroid.com/index.php?topic=241.msg1802#msg1802 suggests the latter is also possible by using
  Code:

  --suppress-warranty-warning

  with the flasher command, I did not check this worked.
• Now again powered off and flashed the openmode kernel with the full images
  
  Code:

  sudo flasher -f -F DFL61_HARMATTAN_40.2012.21-3_PR_LEGACY_001-OEM1-958_ARM.bin -F DFL61_HARMATTAN_40.2012.13-7.ALPS_EMMC_ALPS.bin -k ../PR1.3/maemo.cloud-7.de/HARM/N9/1.3/openmode-kernel/zImage-2.6.32.54-dfl61-20121301

• Happy with my new firmware and openmode I installed some software then figured to restore the backup: Copied back the Backup4 directory from my PC to
  
  Code:

  MyDocs/.backups/Backup4

  where I had to create the .backups directory, since no backup on the newly flashed image...
• Using the internal Restore mechanism I recovered my Accounts, Notes, Contacts, Messages and whatever settings the internal Backup saves that is not so visible. I declined to install the missing software after the phone rebooted.
• Some programs refused to install, e.g AppsForMeego using the MeeCatalog but it did using the "Restore" function in the settings. Some programs installed flawlessly (openssh using MeeCatalog). I guess the installation behaviour is not flash/openmode related.

Astonishing (for me at least) is this:

• I don't get the BigScaryWarning
• I was asked my passwords once and never again so far. (aegis seems to use the openmode security keys and is happy with it)

Update request @jalyst. Since PR1.3 is the last update, would it not be helpful to update the OP to the current kernel?
And: BIgScaryWarning is it not solved? For me it seems so.
I don't know if any of the rest is obsolete.

I think a separate wiki entry for why and how of OpenMode / Injection would be helpful here: wiki.maemo.org
Does that exist already?

Cheers.