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It doesn't matter if you rape Emily or not. But if you let her go with her sister, she will come back either if her loyalty was 25 or above, or if you have helped her with 50 food and 50 gold. Maxed obedience is not enough.
If she didn't come back after 5 days and you don't want to start a new game: open your save, find "sidequests", replace the number next to "emily" with 0 and reload your save. Emily will wait for you in Winborn market again.

Thanks, that pretty mush full answer, have fun