Reawakening: The Side Step Trilogy, Book 2

Reawakening: The Side Step Trilogy, Book 2 by Orson Scott Card

A couple (Laz and Ivy) wake up and try to find their purpose. They are clones of an elite scientist and his assistant. They have their past memories and try to discover their purpose of being revived as clones. The scientist has the ability to "sidestep" to different time streams. The assistant has the ability to identify time portals. In their life as clones they have developed a romantic relationship. (However, it is not until the end that the original join together. They had connected, but felt reluctant due to age and business relationship.) 

In the story, they try to figure out their purpose. They meet with some of their other clones. There is also a mysterious message from a portal. One of their attempts to open a portal leads to some people going in and destroying a school. They send an army back in the portal to crush these people.. They also run into their children. They have some bizarre powers to appear and disappear. The son has a habbit of showing up naked and intimidating. Laz punches him as he is materializing which results in all sorts of internal damage. They then find an appropriate time stream that allows him to be healed, but still remember his bad behavior so that he reforms. In the end they discover the original Laz has traveled in time and feels "stuck". He eventually connects with the real Ivy and they can live happily ever after. 

The book has a number of streams that seem only tangentially connected. The premise is a bit like Mickey7, but explores some different areas of time travel and multiverse.