When I used to play classical clarinet, I played trumpet for a while, and I think it did hurt my clarinet embouchure--but that was only in the sense that it made it hard for me to get close to that IDEAL classical sound I was trying for. It's so much about attempting to reach perfection of tone in that kind of music. But jazz and pop music are much more tolerant about personal approaches to tone--I mean, it's a plus to have "your own" sound in jazz, but don't try that if you're going to audition for a symphony orchestra! Maybe it's similar on flute: if you're a classical player, you should probably stick to flute (and maybe piccolo) but if you're playing jazz or pop, you can just make a judgment call based on whether you personally like or dislike what is happening with your embouchure and your tone. Playing trumpet definitely won't prevent you from playing flute, but you might start to sound different on flute.