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I was just informed that I will need an apico surgery for my #3 tooth. This tooth obviously had a root canal done on it 5 years ago. For years, I've been questioning a bone like mass right near this tooth. My dentist tells me that it is probably my jawbone but I was wondering, could it be a left over root from when I had my widsom tooth pulled? If so, could this be the reason why I have an abscess by that apico tooth?

I love people that think like you and question how things are related. Questioning is how knowledge develops.
From your description, it is unlikely that the bump is from the wisdom tooth or associated with the residual infection to be treated with the apicoectomy. Your dentist should be able to tell you conclusively what the bump is. Hard bumps are fairly common along the ridges of upper teeth and are usually just part of the jawbone like your dentist said. Soft bumps are more common with infection and could be a symptom of a failing root canal.

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