Refuge (Exile) by Stewart, Glynn

A dying world, shattered by a broken machine
A desperate flight, their only hope for refuge
A robotic race, ally and destroyer alike
The Republic of Exilium has grown in strength and confidence at the far end of the galaxy from the rest of mankind, sending out scout ships to survey the worlds around them as they try to learn more about the mysterious Construction Matrix AIs.

Finding one of the genocidal rogues of that mysterious "race" in the process of destroying an inhabited world, Captain Octavio Catalan his ship into a desperate battle. He is victorious-but he is too late. The world of the strange aliens he has encountered is doomed.
The distant Republic can barely help, but the honor of their leaders will not permit them to stand idly by. Ships and crews are set into motion to commence a desperate evacuation of their newfound friends, and debts with the strange Matrices are called in.
One branch of Matrices destroyed the planet. Another may well save it-but the AIs have their own agenda and the price they ask may be beyond the Republic and its new allies…

Glynn Stewart is the author of Starship's Mage, a bestselling science fiction and fantasy series where faster-than-light travel is possible-but only because of magic. His other works include science fiction series Duchy of Terra, Castle Federation and Vigilante, as well as the urban fantasy series ONSET and Changeling Blood.

Writing managed to liberate Glynn from a bleak future as an accountant. With his personality and hope for a high-tech future intact, he lives in Kitchener, Ontario with his wife, their cats, and an unstoppable writing habit.