Dear Customer (name blocked for privacy),
I wouldn't phrase a description of an apicoectomy as simply "nicking" the tip off, although that syntax suggests what is done. Apicoectomy literally means the removal of the apex (tip) of a tooth's root, but involves more than that.
The rationale for the removal of a root tip is that the very end of the root is the hardest part of a root canal to clean and seal, despite the fact that this area is perhaps the most critical to root canal success. By removing the root tip, the part of the root canal system that was not adequately cleaned and sealed is removed-- ostensibly to the point in the root canal where it was adequately cleaned and sealed. Apicoectomies commonly include additional procedures as an integral part of the whole-- it would include the removal of any inflammatory tissue such as a cyst or granuloma, and might also include the placement of an filling at the end of the root canal to improve the seal of the remainder of the root canal filling.
The limitations of apicoectomies are two-fold: first, we know empirically that they don't always work-- presumably because they don't always address the reasons why a particular root canal therapy failed, and second, because they shorten the root of a tooth, and thereby reduce the support of the tooth if it already has a short root.
As for whether an apicoectomy is appropriate in your case-- this is a determination I am ill-equipped to make without looking at an x-ray. However, if that dark area at the root tip is the reason for your infection (a reasonable assumption, although not necessarily the case), then an apicoectomy may well salvage the tooth.
Alas, yes-- a mid-root perforation or root fracture would probably spell the end of the tooth. However, your dentist would probably not have recommended an apico if he suspected a root fracture or perforation.
Hope this helps...
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Mark Bornfeld DDS