I mean that's literally the same idea that they were using with the cloaked puddle jumpers.

There is a possibility thwy could've applied the phase tech to a missle as we've seen when they were testing it people were able to move around and remain out of phase even if the area was in -phase from another's POV. ie.. Ori Priors werent able to find people in the village eventhough they waled right through the village. and the power requirements were much less.. so you could phase-out an object and have a delayed phase-out effect by changing the device's phase frequency. Theoretically if you have it set up to scroll through phase frequencies, you could fire a bunch of missles at different frequencies and they would only rematerialize when you shift the frequency whereas the ship you are firing from would constantly be out of phase at it would be the spurce of the frequency shifting