Stevie, JB has gone back to the X-MEN,  but the X-MEN haven't gone back, so to speak. As JB has noted before, most comics should be read as happening "now" and topical references aren't necessarily meant to tie the story to a specific time period,  outside of an actual period piece.

The way I understand it, the death of Phoenix story wasn't meant to have taken place in 1980, and all of a sudden the Elsewhen stories jump ahead nearly 40 years. All of the stories are meant to be happening during the period you are reading them unless the narrative says otherwise. 

Think of it like this... at Marvel, with the current books, the death of Phoenix happened an unspecified amount of years past, but it's obvious that it was not meant to be four decades in the past based on the age of the characters.  JB is not writing a period piece, he is writing new stories with his team of X-MEN that springboard off the stories when he left the title.