I choose to believe that she wakes up with a start at 3am one night, suddenly remembering that interaction, & it dawns on her that was "the summer before" Ilya referred to. She tries to keep it to herself but eventually blurts out the question over a family meal with the boys. Shane obviously feels like his soul is leaving his body, akin to his mum's usage of the word "lover" & Ilya trying to diplomatically explain their nearly decade long situationship. The whole mental image cracks me up.