Yeah, it's quite a bit unfortunate that all your work more or less is rendered outdated every time patches are released. Maybe avi is the best way to go, for old tracks at least, even with drawbacks like file size and not being able to 'take control' mid track.
The problem with broken tracks after patches has been around since day one, and I'm surprised little has been done to remedy it. After all, it actually also breaks the product itself somewhat, by disabling the default tutorials.
Maybe ED could come up with a track versioning system that keeps separate copies of older flight models (basically just a bunch of dll's I reckon), that automatically kick in solely for playback of old tracks? Has this been seriously discussed before?