Shadow of the Well of Souls by Jack L. Chalker

Immortal, unchanging, the external survivor, Nathan Brazil had tired of his long duty as the guardian of the Well World and had enlisted Mavra Chang, space pilot and adventurer, as his companion and equal, sharing with her some of the godlike power to control the universe's destiny. But over the millennia, Brazil and Chang had become estranged. When they were once again summoned to the Well World, they came as bitter rivals, each racing to be the first to reach the Well of Souls. What they found, however, was a Well World changed in ways it should not have been. Evolution on the Well World seemed to have diverged from its preset course- and that was impossible. Brail sensed that some force beyond local animosity was at work, and he was determined to find out just what that force was and how it could have changed the elaborate programming of the Well of Souls. But the changes that had so affected the Well World were beginning to change the unchangeable Nathan Brazil - and if the watchman himself could altered, the universe might be left without any guardian at all . . .

This book is part of the "Watchers at the Well" series.
Here are some other books from this series: