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Too many to count, though the ones that stand out the most are probably when (as mentioned above) Flute is stabbed in the chest by Hamel but still smiles, trusts him, gets up and takes his hand and when Hamel and Sizer are reunited with their mother.
In the Violinist of Hameln manga, fist volume's last chapter, we're treated to the sight of JerkassAnti-Hero Hamel carrying a battered Flute on his back into the sunset, even though he had been the one to puppet her into a hopeless fight against an enemy he knew she couldn't defeat (throughly played for laughs). (Predictably enough, by the third volume, even a kid they just met could tell they were totally not in love, and mocks them accordingly.)
In the third volume, Hamel's Nice Hat falls off during a Freak Outcaused by the triggering of his demon blood, and accidentally reveals his lone little horn. Raiel tries to calm him down by attacking him with snow dragons, which doesn't work too well; however, upon learning of Hamel's parentage, Flute immediately jumps into the battlefield, hugging him from behind and crying while saying she finally understood his pain. Hamel imediately calms down, puts his hat back on his head, and starts playing his violin for the previously terrified villagers around him. The heroes go right back to their wacky hijinks a page later, but after the tension of the previous chapters, it's almost a relief to see Flute bashing Hamel with her Cross of Divine Retribution again.