I need to fit new intumescent seals to an existing fire door. there are already channels in the existing frame but they have never been used. They have now been painted a few times and would need routing again before the intumescent seals would fit. The company I have approached to install new seals has said it would be easier to route and fit them into the doors. Would the existing channels in the frame need to be filled in or could they be left as they are? 

Presumably the intumescent seal would fill the space in the frame when they expand.

I would take issue with the company. The frame is already grooved, so clean-out the groove for the seals to fit.