MetalPixel: "Your save files get deleted every time? $5 dollars please"
Well, this is
apparantly true for Q.U.B.E. already. It happened to me, too, and since the workaround doesn't appear to work for me, I guess I'll have to abandon the game as I don't feel like repeating all the stuff I did already.
Regarding actual patches and important gameplay improvements, I think the way to go is offer separate versions, that is keep the original version and sell an enhanced version with extra stuff separately, but make sure both versions are up-to-date with the latest patch and the enhanced version only has optional stuff, nothing essential.
I liked how Harebrained Schemes did it with Shadowrun Returns, when the new DLC came with improved gameplay features like a better save system, but those features were patched into the original version, too, even if you didn't buy the DLC.
And publishers should also consider options to upgrade basic versions to GOTY / Collector's Edition / Director's Cut for those who already bought it, instead of making them buy the game a second time.