I thought, not even Zounose can put eating humans into a story about Flan being a dog, right? And I was right! What a miracle that turned out to be.
Canonically, Flandre isn't aware of her meals being human, so something indistinguishable from what it purports to be is exactly what you'd expect:
Speaking of which, she doesn't even know that what she always eats were once living humans. Her daily meals are made to look like foodstuffs such as cake and tea, after all...
Given that she already has half a dozen screws loose, that's probably for the best.