Can I say "Thank you for your flattering comments" without sounding negative?

"Flatter" does not always mean that the compliments are insincere, so your response will often be taken to mean that you are sincerely flattered by the praise you've received. If you wish no ambiguity, then by all means express yourself directly using terms whose meaning will not be misunderstood. @MaxB offers one; others might include "Thank you. I appreciate such positive feedback." Or "Thanks. Your opinions mean a lot to me." And to foster the good working relationship, you might also state that "I welcome any insights you might have that might help me improve my performance further."