Hiya I've done my 2 daily runs of Chao like an hour ago and then went to the lounge to check the recently implemented NPC that tracks limited daily activities like bosses, APQ and Dojo (I haven't played in a while and wanted to see it for myself) and I'm seeing that Chao incorrectly displays as 0/2. I'm not sure if this screenshot helps but it does include the messages showing I picked up the NX in my 2 subsequent runs. I've also done my runs around 21:00 / 09:00 PM server time so it shouldn't have reset already. Dunno if it's just Chao or other bosses as well. I'll try doing other bosses on top of Chao some other day when I get the time.
Thanks for letting us know! We noticed a few boss that doesn’t function as intended too and we are working on it!