Flare's situation might in fact be FUBAR, but one should have
some doubt that the mangaka would doom a character who has played the rôle that she has.
Whatever the
intention of the black pages, they convey no more than
mood.
Right now, what we have is Flare's being told by a hostile alien that she were torn in two, and her
apparent memory of that event. The apparent memory is the datum of greatest concern.
But consider Flare's explanation of Tamura-kun's situation in the final panel of page 123 in chapter 6 of volume 1:
However, the consciousness is a body made of energy — It seems that it'll get weaker if it's separated too long from the body, making it difficult for it to maintain itself.
Tamura-kun was separated from his body
after Flare's supposed death, yet his spirit was dissolving and hers has not been.
Something is different about her situation.
Personally, I'd like not only for Flare to have a happy outcome, but for her senpai to have one as well. That girl was without malice; she was simply too trusting. And, when she saw that her body was about to be used as a passage by the aliens, she cried for her own destruction (page 176 in chapter 8 of volume 1). But the senpai is probably doomed; and, in that context, it is less likely that Flare is also doomed. (That would be four sacrifices from six characters, not counting Flare's dead parents.)