When you say deletion, do you mean server closes and sometime later you restart, and the saves don't work? Or do you mean you broke the checkpoint but you still want it to save whoever stepped on it? The latter won't work.
If you want to have some system to save players level or stage they're in, you could assign them a variable that increases each level they pass, so when they join they can just tp to the level they left off on. It's not the prettiest system, but it works.
Alternatively, you could use this:
http://orbs.daprogs.com/rtb/forum.returntoblockland.com/dlm/viewFile14a6.htmlIt'd let players save their checkpoint to wherever they get. I don't know what you're planning though, so you might have problems with players saving when you don't want them to save or people being dumb and forgetting to save then getting angry.
I'd personally go with the variable saver.