These Backups contain a stock, not-rooted system image that is read-only and the corresponding boot image. Besides they will override TWRP with the corresponding stock recovery during the restoration process.
How to use the Backups/ !!!Warning!!! If you follow my instructions all your data will be erased so backup everything that is important (e.g. contacts, messages, pictures, etc.). !!!Warning!!!
Be aware that you need an external SD card for your phone. (No size limit!)
01. Format your SD card with a PC to exfat and put it back into your phone.
02. Boot to TWRP.
03. Create a backup on your external SD card. (Backing up "Boot" is more than enough. We only want TWRP to create the needed directories on your SD card.)
04. Download the correct backup for your firmware version. (It is stated in the line with "OS" at the beginning when you boot to download mode. The "firmware version" in "settings>about>software information>more" is only the base of the rom you are running.)
05. Unzip the downloaded backup.
06. Copy the unzipped backup folder to "TWRP/BACKUPS/<YourSerialnumber>/"on your SD card. Sometimes this is only possible if the SD card is directly connected to your PC and not put into your phone. I don't know why some M9s refuse the copy process.
07. I recommend wiping everything except "Micro SDcard", "USB-OTG" and "SD-Ext".
08. Check the "Mount system as read-only" box in the Mount menu.
09. Restore the backup.
10. Boot to system (ignore the warning that no OS is installed). This process may actually take a while!
11. Congrats! Your system is now stock and able to receive and install official OTAs, again.