[Samsung Galaxy Nexus] UlixesTNT:
I found the solution to my problem.

It seems that the only way out of this problem is reflashing.

Here's exaclty what I did. I hope it will help someone in my same situation. I DID perform a backup through TWRP before flashing and pulled it through Galaxy Nexus Toolkit (Found somewhere here on XDA) [It could have been done via the ADB tool found in the Android SDK Toolkit, available on Google].

The stock images were found here and then extracted in "...\adb\sdk\platform-tools"

0) Phone Shut Down;

1) Go to Bootloader by pressing: Power + Vol Up + Vol Down;

2) Run the Galaxy Nexus Toolkit;

3) Select current model (mine was a GSM Model 4.2.2);

4) Input Option 10 ("Boot Custom Recovery Without Permanently Flashing it") --> Option 2 ("Boot to TWRP Touch Recovery...") --> type "yes";

5) On the phone, wait for TWRP to be loaded, then select "Backup" and check all the boxes, set the Backup Name;

6) Swip to Back Up and wait for it to be done (It may take a few minutes). Once done, note down the path where the files where backed up;

7) Then, back on the PC and Galaxy Nexus Toolkit (perhaps it may need to be restarted), select Option 14 ("Pull Files or Folders from the Device". --> Option 2 ("Manually Answer Question") --> type "yes" --> type the full directory you want to be pulled onto your PC (for example, mine was: "/data/media/0/TWRP/BACKUPS/016B7378060040" --> Wait, it will take a while depending on how big the backup is;

8) The files that have just been pulled are inside "...\Galaxy Nexus ToolKit\pulled_files_are_put_here";

9) Still on the PC, we open a console instance, we move to the following folder of the extracted Android SDK: "...\adb\sdk\platform-tools";

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We have to make sure that all the .img files we downloaded are exactly in the folder mentioned in point 9), ALL OF THEM (so the ones in the subfolders need to be in the above mentioned SDK folder as well for it to work properly); In my case they were: "bootloader-maguro-primemd04.img", "radio-maguro-i9250xxlj1.img", "boot.img", "recovery.img", "system.img".

Pay ATTENTION: the first two images "bootloader-maguro..." and "radio-maguro..." might be different in name depending on your phone, whereas the othes should be the same. What follows is exactly what I wrote, so the first two images will be the above mentioned: please adjust your command accordingly.

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10) On the Phone (still on TWRP) select the option "Reboot", then "Bootloader";

11) On the PC type:

"fastboot flash bootloader bootloader-maguro-primemd04.img" (Again, may be different in your case)

"fastboot reboot-bootloader"

"fastboot flash radio radio-maguro-i9250xxlj1.img"

"fastboot reboot-bootloader"

"fastboot flash boot boot.img"

"fastboot reboot-bootloader"

"fastboot flash recovery recovery.img"

"fastboot reboot-bootloader"

"fastboot flash system system.img"

The last one may take quite a "long" time, so be ready to wait.

[I know it may not be necessary to reboot every time an image is flashed but that's how I did it, plus anything should go wrong we can get to know what didn't work]

11) On the Phone, scroll down the options by pressing Vol Down (or Up), when you see the option "Start", hit the power button to start Android.

That's it.

I hope it's of any help :).