If a quantum system is described to be only in Quantum states $s_1$ and $s_2$ (described by computational basis $\vert {0} \rangle$ and $\vert {1}\rangle$) or a combination of both (for a qubit system for example), should not all the operators, which we interpret as representations of measurable properties of the system, be only diagonal matrices? What happens if we have an operator whose basis is not the computational basis?
If we measure a property of the quantum system (operator O) and measure an eigenvalue for an eigenvector which is not associated to $s_1$ nor $s_2$, but an eigenvector which is a linear combination of both, does this mean the quantum state collapsed to such eigenstate? Would not that be contradictory to the fact that the only observed states from the Quantum System are $s_1$ and $s_2$?