Hermione, Draco and Theo were in a car crash on Christmas Eve on their way back home from the Granger's home. They were celebrating Bellatrix being found and killed before harm could be done to Hermione. The boys were badly injured in the crash and were rushed to muggle hospital and comatose. Due to the muggle medicine and the potions they were being given, they somehow shared a dream-like state. They dreamt up Hermione's death and going back in time. When they woke, it was only as their "mission" was accomplished. For Theo it was protecting Hermione, for Draco it was not only protecting her but when she placed the ring back on the proper finger after witnessing the memories, it signified that she would truly be his and he was at peace. He dwelled on wanting her over the whole story and she finally was. When they woke, they thought they were still in a world right after the battle, but they weren't.
It was all a dream. They had dreamt from page one till when they woke. The memories in Draco's phial real save for the invented, stress-induced murder of Hermione. We added clues for a while before the reveal with things like 'beeps' while Theo was in the hospital wing and italicized voices he's hearing that were actually voices in the muggle hospital.
Hermione doesn't remember her kiss with Theo or-anything outside of the phial memories-because it didn't happen. It was a dream.
We focused on having lots of memories in the phial that we went into detail about so that there would be a 'root' in reality when they pulled out of the coma. You could say that our awoken Draco and Theo are most like the original two that travelled. When they woke, they identified with the younger two, but as they regained their memories they knew it all. That's why when the babies are born they make reference with, "Five turns should do it, eh?"
With all that said, we leave you with a quote straight from the Queen till the Epilogue:
"Of course it is happening inside your head, Harry, but why on earth should that mean that it is not real?"
It was real for Draco and Theo.