If I change a section a copper to pex then my fixtures on the pex system will not be grounded? Is that a problem . Is there an electrical code covering that

Most houses today are plumbed with PEX. Theoretically there could be an issue but only if a copper plumbing fixture AFTER the PEX connection is contacted by an electrical wire and it shorts. Since the plumbing is probably quite isolated in a bath, I don't think you have a potential, or at least not much. Many houses today are not grounded through the plumbing at all but through buried Rebar encased in concrete and subsequent ground contact. Good intuitive thinking!