Windows doesn't actually support minimizing to tray, instead applications create a tray icon and hide the window(using various methods). Because of this there is no proper native way to restore that window.
Thanks, I did actually find the simplest way to do this. I'm not sure if this is something that the application handles or if windows knows that the application is running in the tray already.
If I open the window from a tray item I can close it, but not minimize or anything else.
I can open it with the .exe file.
I don't know if that is the way to handle it or if there are any down side to this but it works for now.