I haven't watched the anime, so I can only guess at what's happened there so far, but this is what happened in the manga:
- Why are the girls alive again in the end, except one of them?
Because of Hatsuna. Her power grants her immortality and allows her to regenerate infinitely, as long as her Drasil is still in her Harness. Her power even allows her to revive and regenerate someone within 24 hours of their death, at the cost of Hatsuna hanging up and staying in a half melted state until she recovers the next day. She uses this power to save Kasumi who was killed by Valkyria the same day Kotori died.
- Were they succesfull with creating their own pills?
Yes. As a reward for defeating Valkyria, and saving the world by ejecting Kotori, they received the formula for the medecine from Hexenjagd.
- Is it really impossible for Kuroha Neko to regain her memories?
That is currently unknown. We know that Kuroha managed to recover her memories when fighting Valkyria, including the ones from before she became a magic user. That was the only instance where she regained any kind of memory.
Of course, the above answers assume that the anime has been (more or less) faithfully following the manga.