Is "the hole where the tooth had been" acceptable [closed]

Dictionary definitions do not add much to common understanding so I give none. More generally:

A hole is a recognisable volume (or area) in some material where we might (as a possibility) expect there to be that material. Thus we talk of a hole that needs to be filled in the road or of a hole that needs to be patched in a sheet. Once it exists it does not disappear: it can only be filled and there is always a difference, no matter how small, between the filling and the surrounding. There are small differences in the composition of the asphalt or cloth, discontinuities at the join and so forth. It is an adjectivally modified hole: a filled hole, a patched hole.

Not all holes require filling: a hole in a wall may be a doorway; a hole in the body may be the mouth or the anus.

Some holes are transient; the hole we blow in the surface of water fills and vanishes when we stop blowing and cannot be detected (does not exist) thereafter.

So what sort of hole is the one in your jaw? I suggest that it is an adjectivally modified hole - a filled hole. It is a hole that was once occupied by a tooth and is now filled with cotton wool. The volume of the hole was always distinguishable from, and defined by, the surrounding bone. It was filled by tooth and is now filled by wool.