I just encountered this issue with my Dell Latitude E5550 using a port extender and two external monitors.
My problems began when I had a power failure. For silly reasons, I could only plug in one of my two monitors, so I opened up the screen display interface and de-activated the screen that didn't have power.
Once the power came back on the process to turn my screen back on was unintuitive. I couldn't see it in the screen display interface even after rebooting or redocking my laptop.
So I tried
$ xrandr --auto and got Ubuntu to extend to "one" screen but duplicate to both of my externals (they are two of the same model). Amusing but not useful.
It was only when I clicked on "1 Built-in display" like in the screenshot below that I was able to select my "3rd" screen and turn it on again.
The Screen Display Interface
Doing this flipped the two screens around for some reason and I had to rearrange them but that was easily fixed!