The procedure you describe-- an "apicoectomy"-- is a procedure that is typically performed when repeat root canal therapy
is either impossible, unfeasible, or not expected to provide benefit.
Although I cannot conclusively infer that any or all of these conditions were met by your situation, it is likely that your dentist chose to provide you with an apicoectomy for one of these reasons. Assuming that was the case, cleaning
out the inside of the tooth was deemed to be inappropriate. Apicoectomy does not depend on cleaning out the inside of the tooth because it typically includes sealing off the root end and thereby sealing any septic material inside the tooth where it cannot do any harm. Of course, no procedure can offer a 100% probability of success, and certainly apicoectomy is no exception. This is because there are often other locations on the root where sepsis can leak out, but these openings in the root are microscopic, cannot be seen, and their presence often cannot be detected or inferrred. There is also sometimes the presence of other complications, such as undetected root fracture.
Flying on a plane does present some risk of a pain
event when an active infection
is present. This phenomenon is called either "aerodontalgia" or "barodontalgia", and is due to the effect of fluctuations in the cabin air pressure in the plane on the infected tissue. While this type of phenomenon is not a real threat to health, it is indeed a temporary threat to comfort.
I cannot offer reliable treatment guidance in the absence of diagnostic information. However, the failure of the root canal therapy and the subsequent failure of your apicoectomy suggests that your infection will be difficult or impossible to control, and further attempts to salvage your tooth may become increasingly unlikely to provide benefit. I suspect that your dentist may suggest that you have the tooth extracted, because this is the only option that is certain to eliminate your infection. Naturally, if you choose to extract the tooth, your dentist will need to consult with your medical doctor so that your anticoagulant regime can be temporarily modified to reduce the risk of bleeding during the procedure.
Hope this helps...