To make the primary monitor change permanent, go to Menu -> Other -> Startup Applications, and click Add. Give the startup program a name, like "Set Primary Monitor", then in the Command box, enter:
xrandr --output monitorName --primary
where monitorName is the name of the monitor you wish to use as the primary monitor, as listed in the script from this post. My command for example, looked like this:
xrandr --output DVI-I-2 --primary
Your Add Startup Program window should look something like this:
Click Add, and you're done! Let me know if this works for you below!