I don't normally go to that extent. it depends on the situation.
I have never pretended to bee a contractor. I am there to remove bees. I ask them if they have someone to open the section up, handyman, contractor, etc... the answer is invariably no, no one will go near it.
I will open the void up, I will remove the bees and the comb, etc... entirely.
After I remove those, I take a cleaning solution and scrub the former nest area to reduce/remove the nest scent as much as possible.
IF I am able to easily close the void again, I will and I will do what woodwork, etc.. to repair/seal the entrances I find.
If I am not the one to close the void back up, I make notes and identify the entrances and the steps that the contractor/handyman will need to use to seal it properly.
If and when I am the one to close the void, I prefer to do so with solid materials like patching wood, etc.. with same material. I only use caulk to seal up the edges and perimeters, not close holes.