I've made a mistake linking my property calendars that could have resulted in the same situation, but I caught it before I got any double bookings.
This is what happened to me and how I resolved it. It may offer you some idea.
I have a town house which also has two apartments in it.
I set up as the house as the "Main listing" that contains the two apartments. This was done through linking calendars ( I think of sync as syncing with outside calendars, the one for airbnb listings was called linking).
https://www.airbnb.com/help/article/1864
I made the mistake of choosing the wrong listing as the 'container' property (Step # 5 in the article). I had to go and correct it for the calendar to display correctly.
Could you maybe have clicked on the wrong property as I did?
Alternatively, could you have accidentally unlinked your calendars?
It just seems to me this has nothing to do with instant booking but something went awry with the container vs. contained listings. Maybe through a glitch on the site etc.
I hope you figure it out soon and update us on it.