Uh, how exactly should it "check if you loaded the prequels save file"?
I mean it is, after all, but a program, it cannot guess what it is doing or what you want it to do. So there cannot be a magical something that will realise it is a sequel or a prequel or whatever and just take some data from somewhere.
The creators of Mass Effect, for example, clearly had to spend a bit of time in putting these variables into their savegames and then making something that parses this information and makes the necessary adjustments for the sequels. It cannot happen "automatically" - it's up to the user to use the tools provided (like Kyat mentioned, webstorage, for example) to save the data and then see if it's there.