OH SHIT, ignore the red circle, i think i figured it out. Yoshika's dad didn't die, but his mind and soul was transfered into mio's body. That would explain the coincidences as to why they got the letter with the pictures on it, it would also explain mio's feelings for yoshika. The accident at the lab switched their minds and unfortunately loli mio died, but her body survived with the dads mind.
I dunno, but getting trapped in a loli body is hot.