I have completed redrawing all of the frames that have info on them, and my file size has gone down to only 130 mb. Since then, i have not recieved any of those lag-inducing notifications after saving and then closing, also the speed at which my progress saves/file loads in has also gone back to normal. I can use the A and X tools without running into any problems either.
I do wish that in some upcoming update, flipping the canvas could be done simpler and faster than selecting all and manually swapping the sides.