My main setup is an Ubuntu laptop with a built-in screen and a second monitor. Whenever the second monitor turns off, or goes to standby/powersave the laptop detects it as a screen disconnect. This re-positions all my windows and makes a big mess. I am a developer, so I have lots of open windows, and I would like them to stay put.

That said detecting when a screen is disconnected is actually useful when I have to take my laptop places.

Is there a simple command I can use to turn detection on and off? I would like to turn it off when the laptop is sitting on my desk (I can type the command), then turn detection back on when I am mobile.

this sounds weird.
are you using the normal DE that comes with ubuntu these days (gnome, unity, whatever)?
probably an issue with that.

or are you using some sort of exotic monitor?

The problem is definitely monitor specific. Other monitors connected to the laptop do not have the same problem. The monitor is a Seiki 39" 4k TV. It is awesome for everything except this disconnect on standby issue. It also only started doing this after a firmware update, but going back to the old firmware is not an option right now.

so, your system gets confused while interpreting your "monitor's" signals.
i guess the best thing would be to tell your system to not attempt to auto-dis/connect this monitor or in any way try to integrate it into the system.
so everytime you need to use it, you'd launch some script.
but since i'm using neither gnome nor seiki tv's, i can only help in a very general manner.

right, thats the kind of thing I am looking for.