Its been hinted many times that Zhongli's memory is special, so much that I still believe that he remembers Rukkhadevata because his Character Story 5 doesn't consider Nahida as one of the Origina 7 Nahida had replaced Rukkha's existence after the Sumeru Archon Quest

And Zhongli saying that he and Barbatos are STILL the two remaining of the Original Seven despite those events is a proof that Zhongli's memory is unique and is unaffected by Irminsul tampering