I know you can avoid the issue if you use File (which will point to a place in IndexedDB which you can specify as a parameter to its functions) and hard code a path to something like yourName_yourGamesName so it doesn't change when you push an update to your game.
It might be better to see how I did it than try to explain -- this was a sorta slick thing I did when I assumed that most newbies would use PlayerPrefs (like I did in my first game) and get burned by it because it suffers from the same problem you're facing. I basically wrote a script to override Unity's PlayerPrefs behavior and make it write to a location you want. Here's the source code, and the class constructor and Save() function are probably what you want to pay attention to.