Let's say I'm given a two state system that consists of base states $|1 \rangle$ and $|2 \rangle$, those being eigenstates of an hermitean operator $\hat{O}$ that commutes with the hamiltonian, and as well being eigenstates of the hamiltonian, with eigenvalues $o_1$ and $o_2$, or $h_1$ and $h_2$, respectively.
In the Schrödinger picture, the state is evoluted according to the Schrödinger equation. I begin with a state $|\Psi_0 \rangle$ that is evoluted to a state $|\Psi(t)\rangle$.
The time-independent operator $\hat{O}$ defines $|1\rangle$ and $|2\rangle$ as its eigenstates, and then I can write $|\Psi(t) \rangle = c_1(t) |1 \rangle + c_2 |2(t) \rangle$. So in the Schrödinger picture, we know the the relative phases of $|1\rangle$ and $|2\rangle$, and because $c_i(t) = e^{\hbar h_i t}$
In the Heisenberg picture, with our complete set of observables (that commutes with the hamiltonian), $|\Psi_0\rangle$ won't change during time evolution. $\hat{O}$ won't change as well, it commutes with the hamiltonian, and thus its eigenstates $|1(t)\rangle = |1\rangle$ and $|2(t)\rangle = |2\rangle$ won't change either.In this picture, and using only our "complete set of observables" to deduce the time evolution, we can't deduce the time evolution of the relative phases of $|\Psi_0 \rangle = c_1 |1\rangle + c_2 |2\rangle$.
Does that mean our complete set of observables doesn't contain everything that is knowable about the system? Or am I making a mistake somewhere?