So I just stumbled over this myself, and since you never know what people think is worse, opening a new thread to a topic that already exists or posting in a thread that's over half a year old, I'll just go with the latter and comfort myself in having done due dilligence in using the search function first
Anyways, since I also stumbled over the
other thread where several possibilities regarding Calises background are discussed, I don't know if this is really a bug in the "program does things wrong" kind of sense, just a matter of the content not being fully finished and touched up yet, or just a plain matter of a writing fuckup. The fact that it seems that she just pops up in the same state as before the quest suggests a mixture of the former two.
Whatever it is, I think it could do with some fixing up regardless. The most direct, quickfix solution just being a timer of a few days till she shows up again at her spot, best paired with a little notice in bold when you enter the square, noting that Calise is still out of action for at least X more days. Maybe have a text blurb mentioning how Isadora is trying to keep things together in the mean time.
Or use the chance to pad out the content a bit more, have Isadore become interactable in some way, if only to talk about Calises recuperation. Possibly even to the point where towards the end of recuperation there can be an erotic scene or two. And afterwards, of course, one or two talking options to at least recognize that YO, GIRL GOT STABBED.
In any case, aside from the options to do things here, at least a breakoff point for this storyline (or part of it) that is a bit cleaner.