Will dyeing your hair with a permanent dye ruin your natural colour forever?

No, the roots will still grow your old color. If the color has changed when it grows out, it's most likely due to lack of sun exposure. My hair had a lot of red in it before I started dying, and now when the roots show up, it doesn't look like it does so much. If I let it grow out though, as it's exposed to the sun more it gets redder.