(SPOILERS)
I don't really have one canon explanation but more of a mix of reasons! I've purposefully not allowed myself to really decide on all of past Seren's motivations/real feelings, so it mostly depends on how she felt about Yì kǎi.
I like the idea that Seren was also really tired of the scam and starting to feel either guilt or just overwhelmed, and wasn't planning on continuing it like she'd told the minions (at that point she didn't need the scam anymore, it was the cult and minions that pushed her to continue). So depending on how she felt about Yì kǎi, she was using his disappearance as a distraction to upset the minions/Emrys and get some attention off of herself; if she did care about him, it was a mix of that and wanting to put him it to rest, as it seemed his condition could only get worse and he'd never manage to reach the island. (though obviously leaving him in the tower like that is a really cruel way to do this, which goes to show that even in her sympathy, Seren was still a very cold person).
Also Yì kǎi's plan was to stay in Seren's house under a fake identity before leaving the island (with Seren, if they were lovers), and I imagine that would put Seren, the trust of her companions and everything she's gained at risk, so she never saw that plan as realistic in the first place. The plan was more a way to placate Yì kǎi (and maybe make him feel better, if that's something she cared about).
(END SPOILERS)
I hope that's somewhat satisfying :') I'm working on some extra stories for the DLC booklet right now which have some PoV stories for the party members, and I think the first meeting PoVs give a bit more insight into what sort of person Seren used to be! Rhain, Emrys, Aerona and Ikemma's PoVs will show different times in Seren's life and different aspects of her. There won't be super definite answers because I love leaving some questions unanswered, but it might suggest more theories!