Not sure, and probably won't till it's actually released.
Odds are, it will affect the 4.09 versions for sure.
Since they are going to be affecting the core of the game with new aircraft and maps, and such.
The other versions, would be the same. So someone will undoubtedly adjust the files the switcher manipulates for 4.09
I'm sure FT will update the CheckMods blueprint to include the new 4.09, and then we can all run it and update nice and easily.
Jabo