I hope someone can help or even provide a tiny hint (to help me search better) with an unusual startup issue -- I think my phone is starting up in a repair mode, even after flashing to put back into original state.

The detailed story, in case it helps: I had a completely dead battery due to a software issue (two things downloaded from Nokia Store that together had an incompatibility that caused unusually high processor activity and rapid drain -- battery dead and unchargeable after a restart attempt). This was at the time a completely un-hacked N9, fairly new, barely used, no tweaks, no flashing, and working perfectly before the software incompatibility (incompatibility was likely due to two apps wanting to use the sleep screen; this was months ago so I don't want to publicly blame apps that now have newer versions). I am fairly certain that the software compatibility issue caused the high processor activity because I could re-create that issue.

The only reason I added the above detail is that before the catastrophe occurred the phone got hot from the processor working so hard, so I'm worried this may have done something not nice to the phone. Also, I let it sit with the completely dead battery for a week or two, if I recall correctly

To remedy, I had to resuscitate it with flasher (multiple plug-ins needed, so it was "super-dead.") Once the battery was completely charged, I also re-flashed with original firmware and emmc without startup in between. Flasher said "Success" so this seems to have gone well. Again, no hacking really -- I tried to put back into original state by doing this, because after the battery fix it was not normal without reinstalling firmware. How it was abnormal is still the same way as it was before flashing, with symptoms as follows:

When I push the power button to restart, a large tool symbol appears. Then, some text in landscape mode appears, which has things like NOLO and kernel versions, hardware version, etc. The text disappears within 30 seconds or less, then startup seems fairly normal after that. It just seems to be starting up in some sort of repair mode, or maybe something has been corrupted that a standard flashing does not replace.

After the landscape text disappears, although the thing seems to startup fine, each time I shut down and then re-start, it asks for me to confirm that date/time/language settings are okay. After I accept the settings, it seems functional, but with the odd behavior that the charging lamp flashes randomly, not constantly but intermittently. Also, on the back the camera flash flashes red, I think in sync with the charging lamp flashing. I get a similar odd behavior if I plug in to wall charger -- rather than the steady pulsing during charging, the lamp just flashes rapidly.

Also, flashing a new kernel that puts into open mode does not help, and the warranty warning is shown even though I flashed this way:

sudo flasher -a harmattan.bin -k zimage.pr13 --flash-only=kernel --suppress-warranty-warning -f -R

The problem is not the battery because I bought a new battery and that gives the same symptoms.

Would cold flashing help? Or some other unconventional flash? I plan to install Ubiboot to this phone (or at least dual boot, so I can also have the Backupmenu) and I'm wondering if I should just proceed or if the odd behavior should be fixed first.

I hope someone can help with this.