The only reasonable option you have is to adopt the new behavior because it's the correct one, and most probably it's here to stay. Nobody guarantees you the next firmware version will not change the margins, for example because the fab was changed, and thus the order channels in the CFA will change. Your applications shouldn't be designed to relate on mutables to begin with. Now code a converter from old flats to a new format, satisfy your thousands of users, and be done.
The only reasonable option you have is to adopt the new behavior because it's the correct one, and most probably it's here to stay. Nobody guarantees you the next firmware version will not change the margins, for example because the fab was changed, and thus the order channels in the CFA will change. Your applications shouldn't be designed to relate on mutables to begin with. Now code a converter from old flats to a new format, satisfy your thousands of users, and be done.