With the passage of time, of course. The fact that UP and DOWN states (##|1 \rangle## and ##|2 \rangle## in Feynman's notation) are orthogonal does not mean that if you start in, say, state ##|1 \rangle## you cannot possibly end up in state ##|2 \rangle##. It is the unitary time evolution governed by the corresponding hamiltonian of the ammonia molecule that dictates how the initial state evolves in time. The energy eigenstates of the hamiltonian are what Feynman calls ##| I \rangle = \frac{1}{\sqrt{2}} (|1 \rangle - |2 \rangle)## and ##| II \rangle = \frac{1}{\sqrt{2}} (|1 \rangle + |2 \rangle)##, they correspond to energies ##E_{I, II} = E_0 \pm A##, respectively. These energy eigenstates are what we call stationary states; for them, time evolution is trivial and amounts to just picking up a phase factor (it is trivial because the hamiltonian is time independent). It is for these energy eigenstates that the statement "if one preapres the system in the state ##| I \rangle## at ##t=0##, then after some time ##t## one finds the system in the state which is the initial one times the phase factor ##\exp(-i E_{I} t/\hbar)##, and similarly for ##| II \rangle##" is true. These energy eigenstates also constitute a basis, so any initial state, e.g. ##|1 \rangle##, can be written as a linear combination of them: ##|1 \rangle = \frac{1}{\sqrt{2}} (| I \rangle + | II \rangle ##).
Thus to determine time evolution of the initial state one can:
1) expand the initial state in the basis of energy eigenstates;
2) time-evolve the expanded state using the fact that each energy eigenstate picks up a phase factor with the corresponding energy eigenvalue in the exponent;
3) go back to the original basis;
4) interpret coefficients in front of the original basis vectors as probability amplitudes of fidning the system at a later time in those states.