Our expert says:
There's basically zero chance that it's still healing, it will have healed long ago. So either this is a new problem, which may be related to the appendix operation, or it's a new problem that is completely unrelated to the appendix. I wish I could say which it was, but I would be making a wild guess. Is it possible that it's just a stitch, which would be almost co-incidentally in the same place as before. But the fact that it keeps you up at night suggests it is more than this and so I do think that the best is to see a doctor - this is not some mild pain that irritates you when you run, it actually keeps you awake and so it's certainly worth seeing a doctor about.
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