As for the missing nests Owl has been ruled out. Owls don't eat nests. They are carnivorous in other words..meat eater. They hunt on birds, mouse, smal lizard,etc.
Often the missing nests is the work of cockroaches, rat ,ants,etc.
Owl swallows its catches and they vomit pallets which caused by their indigestion systems. With many feathers as shown in the pictures often it is the work of rats perhaps civet cats ( Musang). We have encountered many of the same problems.
Once you have observed this immediate action has to be taken to prevent further damage. A thorough Pest control works is recommended. Rat poison, cockroaches poison,etc all are applied in the Swiftlet farm. Before the Pest control the farm has to be cleaned. Removing all feathers from the floor. 1-2 weeks later to check again. If there are no more feathers on the floor then it shows the predators have been exterminated.
Sometimes it could be both, Rats and Owls. Successful farms having thousand of nests inside and you can imaging the birds dropping of an inches thick. It is very dirty inside if you are not observant enough you may unable to notice the traces left behind by Predators.
(Feathers on the walls too)