I have never heard of this and have no explanation. My first guess is that the events are not in fact associated except randomly; there is a very powerful psychology that attributes adverse events to whatever seemed to precede them. Before I accepted the assertion, if you were my patient I would ask you and your wife to keep a written diary of the exact times of fellatio and onset of canker sores for at least 2-3 months--then would analyze the diary before assuming it isn't random. Another useful approach might be to use condoms consistently for oral sex for a couple of months and see if the canker sores continue.
Sorry I can't be more helpful. Good luck-- HHH, MD
She is probably inadvertently biting her inner cheek/lip and/or the abrasion of the teeth against the cheek/lip is cutting the skin, causing canker sores. People who are prone to canker sores get them almost every time they have trauma to the inside of their mouths.
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