What should I do about my father's rejection of my engagement to a niqabi woman, and my fear that he might ask her to remove her niqab and suffice with a khimar, which might prevent our marriage?

If parents ask their son not to marry anyone but a woman who does not wear the niqab, then it is not permissible to obey them. He must try to convince them and seek the mediation of righteous people. If they insist, then there is no harm in disobeying them in this matter, while continuing to honor them in all other aspects and praying for them.