There is an ongoing long time problem we have occasionally encounter. When we have to import multiple PDF's onto artboards for adding adding cutter marks for printing as soon as you save and close file then reopen it you can see the linked PDF's artwork sizes change. It seems to be relinking to the files and using the bleed size and then reverting to the media size. Has caught us out a few times. It's fine if we import infdividual PDF's.