I am in the same situation. I have created a property on booking.com and the same on agoda also.
And my rooms are duplicated on Agoda. I have on agoda the rooms from Booking and the rooms from agoda, ti is a little mess.
Names and amenties are not duplicate correctly and the price can be different, so it is not interessant to delete the agoda rooms.
And of course when I call Booking or when you arrive to contact the agoda property support (only by mail there is no phone number for owners), they can do nothing.
They should propose the possibility to stop the duplication from booking.com.
I supposed they can control it, because at begining all the rooms were duplicated and now there is only 2 duplicate.
It is very frustrating.
there is also a problem with the names in Agoda that you can choose only from a preselection, you cannot custom them, but it is another story...