You know when I read questions about an unexplained phenomena, I get irritated personally, when people automatically assume that it must be magical or spiritual in nature; not that it couldn't be the case.
Whenever I notice something odd or peculiar I first try to see if there is a logical mundane reason for the occurence, for example depending on the type of wing flapping I am hearing say if it is a light and fast flapping I might look for sign of an insect or insects flying about my house. Some insects can even produce some serious volume from their wings. If it's more of a slower and heavier flapping I might look for signs of bats or birds flying about my house. I once had a bat living inside my house for several weeks that nobody actually saw but we could here something flying occasionaly. But it wasn't until we found the bat nesting in the linen closet that we knew what is was; it just happened to be attracted to the heat from the water heater that was nearby. My point thus is that even if you can't see it at the moment it may just be an insect or flying animal even if you have other odd things happening in your house.
If after a long period and no one can see what it is it could just be a spirit of some sort whether it be of an animal, a sprite, the fae or such lingering about or trying to make itself noticed.