... do you mean why, in terms of the game plot, do things go wrong when you do that, or why did I as the writer make it happen that way?
In terms of the story, it's really just a sequence of unfortunate coincidences. Remember that Janet is totally inexperienced. Hopping into bed with Linds is a huge leap into the unknown for her, and the aftermath leaves her feeling confused and awkward and not her usual assertive self. So she lets him tell her to go back to bed and not worry about what's going on, whereas on the other branch she insists
on being involved. The Janet who slept with Linds is distracted at exactly the wrong moment and loses track of everything else that's going on - and without her actively pushing at people, the experiment ends the same way it always has in the past and the cycle resets.
So it's not because Linds doesn't like her anymore. The problem is entirely in Janet's own head. She would probably get over it in a few more days, except they didn't have a few more days.
It's not really meant to come across as "SEX IS BAAAAAD and you deserve a horrible fate", honest!
Although I know it can be seen that way, and I'm not going to argue with people seeing that there. I knew people would think that and I left it in anyway. You could also read it as "Don't have sex when you're in the middle of a time-travel crisis and need to pay attention."