If you shift click a quest it puts it in you're tracker on the right side, i tried to click on it and the whole side menu pane is gone, if i relog it shows up for a split second but then disappears

Try to reset position, do /questie ingame and you'll see a ton of commands in chat.

/questie cleartracker

is what you need I think. Maybe you encountered some weird edge case and your tracker is minimized.