just tell us that the we can add the boss girls to our harem, like permanent tho, well i just hope u dont overdue urself and keep a bit of ur mortal sanity for urself.
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Yes, conquered Boss Girls can be recruited (some willingly, some you may need to... persuade... or use your Powers on), exiled or killed at the end of the boss fight.
If you recruit them, they appear in the Manor and you will have some basic interactions with them, plus you can bring them into combat with you from that point on (and learn their unique skills, if any) :)