Okay I've been waiting for a looooooong time to post this since I read chapter 93 on May 1st, now let's get down to the business
Because of the time skip, it is safe to assume that the Corp have dragged Annie out of the crystal, I think they did it sometime after the event of chapter 90 where they discovered the ocean, after Eren told Historia about sacrificing her to get the founding titan working, they must've came down with a conclusion to turn Historia to a shifter, by letting Historia eat Annie, but they can't afford to do that before getting some intels regarding Marley's military.
What happened next determine whether Annie live or die,
a. They tortured Annie for informations and decided she's useless
b. They tortured Annie for informations and received invaluable intels and kept her alive for more
c. Annie already died when they get her out
d. Annie escaped from them and hide
e. Annie beg to join them, to see her father but they refused
f. Annie beg to join them, to see her father and they agreed
If a and e happened, then she died...but if b and f happened, she live. It's likely for SC to gain useful informations from Annie but it's unlikely for them to let her join, as the last time they did was a disaster T_T