What does "I'm flattered" mean in context.
For example; you find out someone is developing feelings for you and you say "I'm flattered.. I guess"
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"I'm flattered"; in short, it means the same as "I appreciate it" or "It's nice of you to say"
be/feel flattered ~Cambridge Dictionary
to feel very pleased and proud because someone has said good things about you or has made you feel important
In the context you've provided, "I'm flattered... I guess" it most like means that this person feels both pleased and awkward because, apparently, they don't feel the same about the other person.
It's a very subtle way of rejecting someone ;)