When the big change was done to implement heat a compatibility mode was created. Lots of ideas are being rejected because it would break saves, well, how about adding a program version id to the start of stamps and uploads, so the program can simulate using legacy rules. I don't think I have explained myself too well so:
Stamp Loaded------------------What the application does No ID-------------------------------Load with 46.4 rules ID:47--------------------------------Load with version 47 rules ID:48.......and so on
This way changes can be made without breaking any saves, also there should be a button which allows you to convert what you have open into the newest version, if it breaks then don't do anything, if it doesn't break re-save the simulation and it will use the most current rules.