[LG Optimus L90] mhikel:
Hey guys, I had exactly the same problem. I tried different things including flashing various Roms and Bootstack, but nothing seemed to work. Since I’ve been searching for a solution quite a while, I now have the honor to help you out and everyone with an L90, who stumbles upon the same issue.

First of all, I made a backup of my EFS, so that I could restore the state my phone was in (IMEI=0, but working baseband). You can do that easily with TWRP (thx to shoxxy ;). By the way, this is something which we all should have done beforehand. It would have been much easier to restore our IMEIs.

But don’t worry, if you follow the instructions in this video (https://www.youtube.com/watch?v=nwzgs1Cmr9k) you should be able to get your IMEI working again. For those, who feel more comfortable following written instructions I copied the following procedure using this thread (http://xdaforums.com/showthread.php?t=1960918) as a model and edited them a little to the way it just worked for me.

Do this on your own responsibility! And better double-check with the video our other threads.

Before you start:

Download this package (http://www.mediafire.com/download/figdbxb75j5kyry/package.rar), it belongs to the user who made the video on youtube (PremiumRepair).

Make sure your phone is rooted and USB-Debugging is enabled (http://xdaforums.com/lg-g3/general/guide-root-lg-firmwares-kitkat-lollipop-t3056951)

Procedure :

Install Drivers. Either you use LG Support Tool or download them directly. For me the LGUnitedMobileDriver+3.14.1_ML_WHQL.exe worked just fine. Don’t forget to uninstall old drivers or you could run into problems.

Install QPST v2.7.378. Microsoft Visual C++ 2005 Redistributable is a prerequisite, just confirm it.

Plug your device into your PC (USB port)

Run QPST Configuration from your Windows Start menu. Switch to the second tab ("Ports") and choose "Add new port" (bottom left button). You should see a COM port associated with "USB/QD Diagnostic". Select it, then press Ok. You can close the QPST Configuration window now.

Open Windows Explorer and browse to "C:\Program Files\Qualcomm\QPST\bin" (or wherever you installed QPST) and launch RF_NV_Manager.exe. In RF NV Manager, Go to "Settings / Comport". You should see your COM port in the dropdown box. Select it, then press OK.

Go to "File" and choose "Read from phone". RF NV Manager will read all NV items from the phone. Now if you see item #550, you will be able to alter it (see below). If you can’t find it, go to “File” and choose “Read supported RF NV Items”. If you still can't find it, there is a way to create it. Take a look at the thread I linked to.

Now comes the critical step of altering the IMEI. Select item #550 and you'll see 9 boxes on the right, a "Write NV" button and an "Hex" checkbox. Check the "Hex" checkbox.

Now, you'll have to enter the IMEI in the 9 boxes in a very specific way. The easiest way is to use the IMEI converter (for other method see linked thread). Put your IMEI in, convert it and put the digits in the boxes (two number per box).

Now you can then press "Write NV" to write the IMEI value to your phone.

Once done, unplug the device, and reboot it. Now you IMEI should be changed. If it’s not your number, take a look at the step seven again and check the video.

Please give a feedback, if it worked for you (incl. Details about your device, ROM, etc.) so that other users can profit from it. Thanks

Edit: @ BlackStorm94 - Don't worry about the warning. It will vanish if you install a different ROM.