Thanks! I'm glad you enjoyed it :)

In my head, I don't have details about what happened to Nicholas to cause the retconning. My baseline is pretty much what Nicholas already knows: someone who wanted to get into the Hub thought he would be the weak link in Torchwood's chain, so they abducted and tortured him. The team naturally found and rescued him, but by then Jack wasn't actually sure Nicholas could recover. Essentially they reset his brain with the retcon.