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That does not sound like a reaction to the flu shot.
That being said, I'm not sure what could be causing swelling of his upper lip the comes and goes without any other signs or symptoms.
If things persist he should see his doctor on Monday. Of course, should he have any problems breathing, the swelling get worse or you are more concerned, he should go to the ER>
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Thanks for replying so quickly! Sounds like nothing too serious, just can't figure out what could cause it.