What is the difference in meaning between these two sentences?
I didn't know you weren't in.
I didn't know you wouldn't be in.
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I didn't know you weren't in. This means that the speaker thought someone was "in" when they weren't.
I didn't know you wouldn't be in. This means the speaker predicted that someone would be in, but they wouldn't be.
The difference is in when the speaker thought they would be in: while they were thinking it, or later on.
I didn't know you weren't in is pretty non-specific. It may be that you expected your friend to be in and decided to visit him on an impulse but he, not knowing that you were coming, decided to go out on an impulse. In other words, the whole thing was an unfortunate coincidence and it was nobody's fault.
I didn't know that you wouldn't be in implies that your friend had already planned to go out but you expected him to be at home. You could, perhaps, have found this out had you bothered to ask him or if he had bothered to warn you. In other words, it was someone's fault - either yours or his, or possibly both of you.