IF I understand you correctly there's a "don't run muted fx" and a "run fx on stop" (not near reaper to check names though) but they should help.
Also if the takes are not being used or muted they shouldn't take up any processing power.
Uploading an image might help me and others see what your trying to do as I feel I've misunderstood you
also you can bounce track fx to a new take to stop them eating processing power (but I think that defeats what you want to do right?)