So ignoring the fact that I have no ideas about if this would work:
Continuing the work on the ender chest idea, what if instead of all items being removed from the beacon and transported to a chest, and the other idea with dropping your items in a special chest every time you log out.
You in your beacon ui could designate and amount of items/blocks/props as important, all items have a set value and only up to a certain value can be protected but that threshold grows as the player progresses, (this could probably be based on the total value of stuff inside the beacon) and when the beacon dies all these items is then trasported to the before mentioned chest, if some of the items is not in the beacon or some points are not spent the game will automatically remove stuff of the highest possible value until the full point vlaue is reached.
Does that make any sense`?