This is the Forever series by Craig Robertson. The follow up series where he has to protect the children is the Galaxy on Fire series.
The Forever series opens with The Forever Life:
Immortal, alone, and broken. To live forever, love must die. Major Jon Ryan is a cocky fighter pilot turned astronaut. He volunteers for the most ambitious, desperate mission ever conceived. The planet Jupiter, thrown off orbit, will destroy Earth in less than a century. Project Ark is humanity's only hope for survival. Jon will search alone to find a suitable location for human resettlement.
To be able to do this, he must first have his consciousness transferred into an experimental android host. He understands the implications of his mission all too well: He will not age and by the time he returns home all the people he knew will be dead. His only companion on his fifty year voyage is his ship's irritable AI.
Jon not only pushes the extremes of human technology, but the limits of his psychological strength. As time goes by, all communications with Earth gradually cease, leaving him in an eerie silence with more questions than answers. Will he save our species from extinction or be the sole survivor, lost forever in space?
The first book in the Galaxy on Fire series is Embers:
Jon Ryan was supposed to be dead. He wanted to be dead. But Jon wakes up in the far future with an alien burrowing in his chest for salvage. Someone was going to pay for this. Check that. Lots of people were going to pay for this.
Jon was the first astronaut to download to an android host to find the population of doomed Earth a new home. But that was so long time ago. He is now literally lost in time. The far flung future is dominated by an unstoppable species, the Adamant. They have conquered most of the galaxy. No civilization has successfully resisted them. Brutally efficient, selflessly devoted to their empire, and callous to all other forms of life, the Adamant have advanced without boundaries. But they are about to run into a major problem. One very pissed off Jon Ryan stands in their way. He escapes their prison ship, rescues two teenage shapeshifters, and intends to protect them at all costs.
Jon, Mirraya, and Slapgren race across the galaxy always just one step ahead of disaster. But the combined evil forces that pursue them tear the trio apart. The teens must fend on their own in a hostile universe. All the while, Jon runs for his life, hoping against all hope to locate the teens. In a galaxy burning with war, genocide, and hidden magic, can Jon Ryan pull off one more miracle?