Post-measurement, we will find the system in state $\phi_i$ with probability $|a_i|^2$.
Almost, the correct final state is $$a_i\phi_i,$$ it's just the result of applying the projection operator. If we wish, we can then normalize it to $$\frac{a_i}{|a_i|}\phi_i,$$ but we should only do it if we know we won't be comparing or superposing it with other states. When we normalize it, we divide it by a real number, which does not remove the phase. The overall phase is not important only if we don't plan to compare/superpose the state with other states.
One way to see that the final state is $a_i\phi_i$, or if we wish its normalized cousin with the phase intact, is to imagine first that all but the $i$th coefficients $a_j$ are 0 and consider the overall post-measurement state of system+apparatus. By continuity, immediately post-measurement the overall state is exactly the same as immediately pre-measurement (we are talking about instantaneous collapses in this question). Therefore we should assign the post-measurement state of the system to also be what it was immediately pre-measurement, $a_i\phi_i$. Anything else would be a bizarre ad hoc unnecessary step.
For the general case, with non-zero other coefficients, the same should be true by linearity, because collapsing the state just means keeping only one of the resulting branches.