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Is it possible that the pain and swelling is the result of external forces causing internal irritation? Like the elastic band pressure of whatever you are wearing? I had found that certain clothes caused irritation because the waist height caused pressure at the bump left by the original direct hernia area. In my case though, there is still a piece of mesh at that spot. This lasted for years and has only resolved recently.
In other words is there a correlation between clothes and discomfort. I remember that you run a lot of miles on a regular basis. A small force might have large consequences. It might explain the seeming randomness of the problem.
I am just past five years since mesh removal and the last six months have been pretty dramatic in terms of improvement. I am doing much more and feeling fewer delayed after-effects. It might be both heartening and disheartening to suggest that you wait. If you do find a correlation with clothing or certain activities it might be worthwhile to avoid those for months at a time then retry later. See what happens.