I deleted an old avvie to create a new Gehn27 testing avvie, and when this brand new avvie arrived at Relto right at the start of the game, with no Ki, the markers from the Anniversary marker quest were already loaded and my avvie was able to collect one of the island-hopping markers. I opened the Anniversary Quest Kimail but it stated that I had to upgrade my Ki to play the quest. So I collected my Ki, went to the Great Zero antechamber, started calibrating my Ki, and successfully collected my first GZ marker. I thought this would mean that the Anniversary Quest markers would disappear, but I seem to be able to collect both types of marker at the same time, with the Ki display swapping to show the correct number collected (but staying the same purple colour - having started the GZ marker quest as green).
I don't know if this is a glitch, related to my having deleted a previous avvie, or whether this is intended, but I thought I'd flag it, as I haven't experienced this before! And having both sorts of markers on display might confuse new explorers?