Call me naive but couldn't you just perform a Short Open Load Through calibration on the VNA that you used to measure the filter? It will push the reference planes (ideally) to the ends of the connectors so you won't have to worry about de-embedding (unless you're in a situation where you cant re-measure the filter). It's a different story if you're using a test fixture where you can't eliminate it.
When you say "phases", do you mean the phase propagation constant? or the total phase change for the length of coax that you're using? That would be the electrical length if its the latter.
Either way, you'd need to find both terms of the complex propagation constant, both alpha and beta. Alpha is measured in nepers per meter or about 8.7dB per meter. You can then find alpha, and you already know beta.
Am I understanding this correctly? I'm a bit confused by the wording: Are you trying to shift the reference planes to the end of coax connectors, or do you have a filter that you want to remove too?