In my case both of my nands are linked so fbi shows up in both sysnand and emunand from when i installed it in rxtools emunand. If i boot into rxtools and choose dev mode for sysnand and run fbi to install sysupdater would it run that way?
You can try, in my experience when I had my nands linked the stuff I installed to emunand showed up in sysnand but couldn't use it unless I tried installing it again in sysnand.