Maybe I mis-understood you… I understood the scenario to be that you got a different route in a clearance from ATC, so then you re-file a flight plan with that route. In that case, there’s no need to refile since the purpose of filing is to let ATC know what you’re requesting, and in this case that’s irrelevant since they’ve already told you what your actual clearance is. You would just modify the route in your FMC / GPS / panel setup as necessary, and off you go.
You file a flight plan to request a clearance. When you already have a clearance, filing again has become unnecessary, is what I mean.