I) Let us reformulate OP's question(v1) as:
What time differentiation symbol should one use on the right-hand side of the time-dependent ket Schrödinger equation?
Answer: Whatever symbol that means $$ \lim_{\Delta t \to 0} \frac{|\Psi(t+\Delta t )\rangle_S-|\Psi(t) \rangle_S }{\Delta t},$$
so apparently both OP's suggestions work. Here the subscript "$S$" (and "$H$") denotes the Schrödinger (Heisenberg) picture, where bras and kets evolve (are unchanged) and operators are unchanged (evolve), respectively.
II) Let us mention for completeness that in the Heisenberg picture,
$$|\Psi \rangle_H\quad \text{does not evolve in time},$$
$$ {}_H\langle x,t |\quad \text{does not evolve in time},$$
$$ \psi (x,t) ~=~ {}_H\langle x,t |\Psi \rangle_H,$$
$$ {}_H\langle x,t |\hat{x}(t)~=~ x ~{}_H\langle x,t |, \quad \Leftrightarrow \quad{}_H\langle x,t |\hat{x}(t)|\Psi \rangle_H ~=~ x \psi (x,t), $$
$${}_H\langle x,t |\hat{p}(t)~=~ \frac{\hbar}{i} \frac{\partial}{\partial x} ~{}_H\langle x,t |, \quad \Leftrightarrow \quad{}_H\langle x,t |\hat{p}(t)|\Psi \rangle_H ~=~ \frac{\hbar}{i} \frac{\partial}{\partial x} \psi (x,t), $$
$$ i\hbar\frac{\partial}{\partial t} {}_H\langle x,t | ~=~{}_H\langle x,t |\hat{H}(t) \quad \Leftrightarrow \quad i\hbar\frac{\partial}{\partial t}\psi (x,t) ~=~{}_H\langle x,t |\hat{H}(t) |\Psi \rangle_H~=~(-\frac{\hbar^2}{2m} \frac{\partial^2}{\partial x^2}+V(x))\psi (x,t) .$$
For a full explanation, see e.g. J.J. Sakurai, Modern Quantum Mechanics.