Consider a time dependent Hamiltonian $$\hat{H}(t)=\hat{H}_0+\hat{V}\tag{1}\label{1}(t)$$ where $\hat{H}_0$ is the unperturbed Hamiltonian, for which the eigenvalue problem has been solved $$\hat{H_0}\lvert\phi_k\rangle=E_k\lvert\phi_k\rangle\tag{2}\label{2}$$ Suppose that at $t=0$ the system is in the $n$-th eigenstate of the unperturbed Hamiltonian, i.e. $\lvert\phi_k\rangle$. Then, as this is not an eigenstate of the total Hamiltonian \eqref{1} it will have non-trivial time evolution and at a time $t=t'$ the state will have (in general non-zero) components $c_i(t')$ along the other eigenstates \eqref{2}, which can be calculated at first order using the usual formulas. Up to this point everything is fine. What sounds weird to me is considering the modulus squared $\lvert c_i(t')\lvert^2$ as a transition probability to the $i$-th eigenstate \eqref{2}.
According to the postulates of quantum mechanics, after measuring an observable represented by $\hat{A}$, the state will collapse to an eigenstate of that operator and the outcome of the measurement will be the corresponding eigenvalue. In our case, the observable we're dealing with is energy, which is represented by the time dependent Hamiltonian \eqref{1}, so the outcome of the measurement at $t=t'$ will be an instantaneous eigenvalue of $\hat{H}(t')$ and the state will collapse to an instantenous eigenstate.
On the other hand, saying that $\lvert c_i(t')\lvert^2$ is the transition probability to the $i$-th eigenstate of \eqref{1} at time $t=t'$ makes it sound as if measuring energy at $t=t'$ could make the state collapse, with probability $\lvert c_i(t')\lvert^2$, to $\lvert\phi_k\rangle$ which is not an eigenstate of the total Hamiltonian \eqref{1}. This would only make sense if the Hamiltonian were just $\hat{H}_0$. Once again I want to clarify that the problem is in the probabilistic interpretation (collapse) we're giving to this coefficient because it apparently contradicts the postulates of QM. Are we measuring only the $\hat{H}_0$ part somehow? What is going on here?