My current best guess…
At some point Henry leaves SB, moves to Seattle, Lucy finds him (with a totally different book than the one Adult Henry gives her to guard)
The book Lucy has is one that Henry had published in the real world (because Author), after he left SB. He left SB after Emma died (not by any magical means, just natural causes of some description, which can be covered in a flashback when JMo does her one ep), and wrote the book as a type of therapy.
He meets Lucy’s mother, not realising she’s someone from FTL. They fall in love, she ends up pregnant, but leaves and goes back to FTL before Henry ever knows that he’s a daddy.
– They have some sort of adventure together and wind up in the EF during “a time of great upheaval”
Lucy grows up in FTL, and when some bad crap starts going down, and her mother is in danger, Lucy escapes to our world to track down her father and bring him back to FTL to help save the family he never even knew existed.
–Henry and Lucy’s home is attacked
–Tiger Lily finds Lucy
After Henry goes missing, Lucy/her mother/Tigerlily/etc need help finding him. So they put a call out to Regina, and of course she’ll go to help find her son. She leaves Snow to run SB while she’s gone. With Emma dead, of course Hook will go to help save her son in her stead. He leaves Charming to be Sheriff and look after SB while he’s gone. And by then Rumple has had some time to experience what it is to have family, so he’s not as dismissive of Henry needing help any more. Also, they could do with all the magical help they can get in they’re gonna be in FTL searching for Henry who was taken by some magical being of some description.
So that gets our 3 returning regulars in position for the whole plot of the season, and there’s believable reasons why the non-returning regulars aren’t around.