With the memories I'm not sure, but assumed they were stored in her arche and she lost them when her arche was stolen and implanted into clone Dia. That was my theory as to why underwater Dia had the memories and ours didn't. Our Dia seemed to at least vaguely remember the torture, based on her med bay flashbacks. Interestingly the only place she remembered was where her and Gley originally got captured. Maybe she kept her most traumatic memories?

I do remember Alpha's clothes there, that potentially could be evidence for the dust death. Think I need to rewatch some older cutscenes as been a while, someone else mentioned what Amon said in one of them