I had this problem - my booking.com calendar was fine, but all my booking.com bookings dropped out of my Airbnb calendar.
I noticed when I received two Airbnb bookings which double-booked on some dates that I had already taken booking.com bookings months ago.
I contacted Airbnb to ask why their calendar was not picking up Booking.com bookings - they said it was Booking.com's fault.
I manually put all the Booking.com bookings in my Airbnb calendar and I contact the two guests who had been double booked. Airbnb agreed to cancel them without penalty to either them or me, and I have booked them into another flat I have.
BUT - in the meantime, their original Airbnb bookings are shown in my calendar as "£0.00 CANCELLED" - but the dates are shown as NOT AVAILABLE. I cannot override this - I have contacted Airbnb daily and they have failed to reply or do anything about it.
I manually changed them to AVAILABLE on Booking.com, but everytime it syncs with Airbnb, it flips back to "Airbnb booking" on Booking.com.
So now, through absolutely no fault of my own, I have empty days which I cannot fill on either Airbnb or Booking.com - and despite being a SUPERHOST and having a 4.9 star average, Airbnb JUST WILL NOT REPLY TO ME.
Anyone got any advice for me???