Try this workaround:
"Delete all the lines after "ui_print("Verifying the updated system image...");" until "show_progress(0.020000, 10);". once you have done it save the file and copy it back into the location inside the rom zip file and flash it on your phone."
Worked for me.
Quoting from official Cyanogen site
Nightlies are not recommended unless you can handle issues arising out of it, since they are not tested
...We have the Nightlies, which are as volatile as a firmware can get. These releases keep coming at an interval of a day or two and if you do end up trying one of these, do not be alarmed if your device goes cuckoo ...
I'm not entirely sure why this worked but what I did was to:
Wipe data from the secondary ROM I wanted to remove
Reinject the current boot sector
Then I rebooted and was able to successfully remove the ROM via TWRP.
Omnirom is already rooted, if anything you might have to install SU.
as to the problem with your primary ROM on multirom, reflash the primary over the top of itself, then when complete install multirom again. As long as you didn't wipe data, your other ROMs should still be intact.....my primary ROM in multirom got glitchy, so I did what I recommended to ...
The answer to your question is extremely complex and (in my opinion) not material for SE since there are a lot of files that you'd need to download and cannot be hosted here. Fortunately, XDA has a thread for multi-booting on the GT-N7000. I also found this tutorial on YouTube so that you can see how its done.