I think there's a way to have a one-time popup when loading a game.
From my limited understanding, I think it works something like this:
It runs a check for a variable when a save is loaded. If it doesn't find it, then the popup appears (I say "popup," but it's just a dialog). Then you can tell the player what you need to and throw up some prompts for them to fill out all the previously untracked variables.
I've seen other devs do it before when they release an update but forgot to track something and so they throw that in there until they can get an actual fix in the next update.