but still, when they released DOE EE they said that we will get "new game" in steam library instead just paching on old file.
(unless I forget to uninstall it

Because it was a new game, it wasn't a patch. You can check; you should still have both the original and EE as separate games and they also have their own achievements.
This is just a release patch. Technically there's nothing wrong with the codgy old techy's mentality of "always start fresh" there's less reason for it every passing year. You're going to get patches automatically anyway, what you going to do then, uninstall the game just in case? No, you're just gonna let it patch.
The way the patcher works is that it rewrites files and adds those it needs. If there's still a problem, I'd verify integrity before reinstalling the game as it can just re download missing or broken files instead of the whole thing.
So yeah... starting fresh install technically isn't a bad answer, it's just a highly inefficient one.