If I understand correctly, save file structure and data is changing from one version to another.
It's a reason why savegames from prevoius release are unusable.
It's good when some of most irritating bugs are fixed.
But it's nevertheless annoying to abandon game and start everything from the scratch.
Is it possible to supply new versions with a simple (maybe even command-line) tool for converting old savegames to new format? At least geoscape saves, not combat?
If not, maybe include a version info in savegame, just to check when load and exclude situation when user guessing "is it a long loading process, or a bug, or I mistakenly selected a save from previous hotfix game?"