It's been almost 17 years since Lily died, and about 2022 since Snape was rejected by Lily in fifth year after O.W.Ls.
Patronuses change after a great shock, and emotional upheaval (from HP6):
“Tonks’s Patronus has changed its form,” he told him. “Snape said so anyway. I didn’t know that could happen. Why would your Patronus change?” Lupin took his time chewing his turkey and swallowing before saying slowly, “Sometimes . . . a great shock . . . an emotional upheaval . . .”
It's not normal to be in shock for 17 years after a breakup, or to still be in love enough for a Patronus after so much time. Obviously Patronuses revert back to original form once some of the grief of the loss has worn off.
He's not saying "after all this time, you still have a reason to be loyal to me?" he's saying "after all this time, you grieve for Lily Potter?"