I remember I have bought this from the developer's website while the game wasn't fully complete. It was an awesome game, but because it was done in Flash, it had a pretty weird saving file system which was rather troublesome. Is it still in Flash now?

And also, how has it changed since earlier versions?

Bought it yesterday, didn't know it before.

The game is still flash, but standalone without a need for a browser. Didn't encounter any saving problems yet, it's just the save is lost after death due to perma death. Also I would be surprised, if it wouldn't be flash sometime anymore. I guess, that would mean a complete rewrite of the game.

My problem with Saves was that I have programs on my computer that routinely wipe cookies and other tracking/spying devices which includes Flash's saved content. And since this game uses Flash, I would get my progress wiped out. Eventually I figured out a way to exempt particular files from deletion, but the game was keeping I think like 5 or more "slots" which were different folders, and would recreate new ones with different name while you played, so I couldn't even easily exempt it from deletion.

You can try the fan-created NEO Scavenger save manager:
http://bluebottlegames.com/main/node/1280

One of the reasons I made that Save Manager (though it's really just a somewhat complex .bat file, not a real program) was because my own cache cleaner deletes NeoScav saves!

Hope it helps others keep their saves safe, too!

Huh. I'm a mod over at the official forums, and this sounds weird to me. It shouldn't be happening. If you try it again and it happens again, pop over here and let us take a look at what exactly may be happening. Things may be a bit slow over the holidays, but the dev is pretty hands on and fast with technical problems the rest of the time.

As for what has changed, that's a pretty large and extensive list. Even if I shorten it to "What has changed since the summer", we have a bunch of new encounters, the ending of the story, new creatures, new crafting, new items, new mechanics, UI changes, a bajillion of rebalances, etc etc etc.