In cycle 1, Yuno has become god and the Deus is dead, and after that, Yuno enter cycle 2. Why Deus is still alive after he is dead?

The same confusion also applies to the Deus in the cycle 3. The cycle 3 take place after Yuno and Yuki killed other diary holders, at this moment, the Deus in cycle has 'died' or become a red crystal-like stuff. How come in cycle 3, Deus still exists? 

Furthermore, Deus is said to be the manipulator of space and time, both of which are eternal, and even so, they is mortal! The logic and causality of this premise seems quite messed up to me.