Hi there!
Years ago, I encountered this strange sounds in the second mission of the game and I don’t know if there is someone who has also noticed it.
It sounds like some birds flapping their winds (maybe are sounds from the birds of the church from the beggining)
Since this is a dusty old building and the sound effect is heard when you enter the loft, I would guess it’s an intentional choice to give the impression of birds flapping around in the rafters.
The devs probably felt it wasn’t worth adding visible bird models up there, but they just wanted to give the player a sense that birds had snuck into the building through holes in the roof.