Other ways of looking at it:
Maybe when she came back she was picking up the change in your phero-signature and not understanding what it was thought YOUR feelings for her had changed. And if you did not send out strong enough a signal that you were still good friends because you thought the change in her was aloofness …
Maybe she was looking for something more than friendship all along and in the month she was gone had time to reconsider given the friendhsip was not going in the romance direction …
And then you have to think about what was the friendship based on and how deep was it. Some friendships are seasonal. I have moved around a lot and have made a lot of friends. But I have not kept up with a lot of them. Why? Because the friendships were based work, on the here and now, on the shared work situation as opposed to outside interests or outside shared values. That does not mean they were not real, or were not good, or even that they were shallow but they were situational.
Mark - you already went into trimming facial and palm hair in another post - to I will leave this part alone - lol.
I think Mark is basically right here also.
First, I really believe that pheromones only enhance who you are. But you still have to be and do to take advantage of the edge they give you. Sometimes they even enhance your bad moods. Mark can attest to that too.
They sure did not have women falling at Mark’s feet when he was in a bad mood. If it was all pheromones then all the friendly pheromones he had on should have had them dropping at his feet despite his bad mood. But they did not. So - they only enhance, and sometimes they enhace something you do not want them to enhance. But they only enhance.
Sometimes in certain environments we seem to hit it off with people but then find outside that environment that we are not matched well. Probably happens all the time in club environments. Guys complain constantly about getting bad numbers or girls “flaking” on them on follow-up. Women complain that guys were not “who they seemed to be” the night they met them. So all the enhancing in the world will not change the fact that while you had a good time together last night in the club, you are still not a good match.
(Note: Off subject - but women can often sort this out before guys can. Or as is quite often the case, they were just out for some fun one night, and while you were fun, you really do not have a place in their life beyond last night’s fun. We always hear about guys who are “cads” when they treat women like this but I think it happens with women a lot more than they usually admit. At least to guys. Now - Back to our regularly scheduled programming 
But this friendship seems like it was too long for this to be the case if you had time to become really good friends. This tells me that while the pheromones might have been enhancing who you were she had enough time to figure out who you were and liked what she saw. So if she has pulled back since her vacation, then it is for some other reason than just the pheromones. I listed several that came to mind immediately, but there could well be others.