Has anyone used 2 16,000mah packs at once on an S900? I'm rebuilding an S900 for a coworker that was bought used and it has 2 battery trays installed on it, and a Y-harness to connect the batteries in parallel. I think this would exceed the payload capacity... but I could be wrong. My coworker swears up and down that it flew with 2 16,000mah Tattu batteries.

Be careful.   if the voltage between two batteries are not equal/balanced and connecting in parallel meaning electricity will flow between the batteries.
I tried this to extend the flight time but the system became unstable, this may due to quality of batteries.

I have flown with that configuration and I have had an autonomy of up to 44 minutes, without any problem

How did you install 2 16000mah? I am interested in extending flight time and redundancy. Have you got a picture?