Yeah it was referenced, but Cindy's pheromones were never activated while she was around Peter, and he did show up once or twice, so Thompson quietly got rid of them.
It was referenced in the first issue:
But she just says they "had a thing", only aluding to the pheronomones.
And yeah, it's never explained why she's uncomfortable around Peter, they look like exes, which, in a date-rape way I guess they are? I dunno, it's weird.
He just says "I assume you're not a clone?" when meeting her before she says anything, so he was just checking there:Like there was literally that moment in Clone Conspiracy where Peter was able to tell she wasn't a clone because she was being abrasive towards him .
(Clone Conspiracy#5)
Silk version of this scene from her comic has the same dialogue too, while ironically enough, not having the same haircut lol.