This game is still in "Early Access" = it is in 'active development'.

While it is understandable that dedicated players want to save their 1000s of hours they already put into the game, I feel there is no (technical) obligation to 'stick' to the old saves ...

... ever.

Games in active development are subject to MAJOR changes in all aspects? Design. Mechanics. Heck, even low-level code? If there is a better, more efficient way to package game data - go for it!

If the changes are significant, there can be no player expectation to hang on to 'old saves'?

This might pain your most dedicated players today, but you - the devs - have to think what is long-term best for THE GAME. :)