The only reason I didn't replicate yet was because I didn't feel like losing more of my only working water containers until I get more spare leather.

The cooking pot holds 500ml of water. The NWP holds 500ml of water.
Filling a cooking pot with water from a NWP causes it to be consumed i.e. a can of soda. It disappears from inventory and is deleted. My guess is that the NWP needs to have some configuration either with the cook pot or Natural Water Pouch. I believe there was a similar issue with Canteens or Water Bottles at one point where they were being consumed upon certain actions with other items that depleted everything in the container but I can't be sure.