Sara admits to Akira that she lied about going a long time without sex, and that she was afraid he'd judge her for it. Which begs the question as to with whom she was having sex when no one came to the bar in the first place. The condoms though were all
way past their expiration dates, if I recall correctly that's why Sana apologises later.
A condom is valid for a long time though, and it wouldn't make sense for it to be resets interfering with it (otherwise it would interfere with expiration dates for everything). So either Sara was so poor that she was using old condoms to have sex with another man just before the resets started (and in her mind that's recent), or she's having a dude on the side (which would be even more unlikely, actually impossible from a narrative cohesion angle).
The thing about goodnight is that Sara's scene doesn't have a check to see if she's having sex with Akira, which would make it possible to not be his child. Which would make it possible for one of the "Akira's girls" to be carrying a child from another man, which I
very much doubt would happen in LiL.
What "The dark. The light" says to her is "why does it have to hurt so much", which if I recall correctly is mostly a chapter 1 thing. Maybe
aramaug is able to take a look at what it references exactly, since he's just done replaying through it. I don't recall if it was ever revealed what it means, or to whom it refers.