To what purpose would the replacement serve? But before answering that question, why do you desire to disturb the arrangement that you have in the first place? Is there a problem with it?

Do you mean that the membrane you have now is just a plastic sheet rather than a proper membrane that will let the rain through? Obviously its possible to sweep up and collect all the gravel and replace the membrane if you want to but it won't be easy, especially if it covers a large area. Have you planted things through the membrane?