Yeah, I wasn't thinking about what you're doing with Tusky, though it's obvious why it's in the forefront of your thoughts.
Having a version number for your pref format and checking it's <= the supported version is an eminently sensible starting point.
I implemented something similar to that at $DAYJOB for configuration/pref files years ago.
I'm mostly just musing about how Firefox could do better if they wanted to.
@mcc
This gave me an idea you could play with for Tusky, for your case where you frequently roll backwards/forwards:
Instead of versioning a pref file as a whole, suppose you versioned it by sections? E.g, start with a recent past version, vN:
* Section # 0 is baseline preferences, that all versions support and you can always preserve.
* Section # N includes all prefs vN supports, so any fairly stable pref is preserved.
* All newer prefs go into a section by SW version which added them.