Emma's quest line can be a real pain to do correctly.
if I remember correctly you have to finish Emma's rout before the Samantha revenge rout what i would recommend is to do the Samantha rout up to the Samantha bj 1 or 2 event then finish Emma's rout before continuing Samantha's rout.
there's also a later event where she can leave the game is any of the other girls have the girlfriend, fiancée, mistress, pet or sex slave statuses which makes her rout especially annoying.
the best course of action if you want to get Emma and do the other harems is to do Emma's rout first until you finish the judgment event then do the other girls.
but for the problem your having specifically is to do Samantha's rout up till the Samantha bj 2 event then do Emma's story line until you have completed the (to be or not to be) event or until the (the judgment) event and then continue the other story lines.
I would also recommend keeping Emma's
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page open so you don't accidently screw up and lock yourself out of her rout.