I am an amateur but is there a foot switch that has an fx loop on it so when you change your amp from distortion to clean you can bypass around the pedals going into the front of the amp and you won’t have overdrive on the clean tones.
I think, to answer this question better it might be helpful to understand what gear you have. In particular, what amp?
Pedal switching systems are what you want to do this seamlessly. Think Boss MS-3/ES-8 or TheGigRig G3 if money is no object. Any of these will allow you to switch channels on your amp using the control outputs or MIDI while simultaneously switching in or out effects in a loop, either in the amps effects loop or in front.
I went down the multi-FX path with Boss GT-1000, which can do the same thing for two loops but includes a gazillion effects as well.