After the Human-Covenant War, what colonies were not glassed? Were there any humans that still lived on these planets?
There are planets which never saw a Covenant ship during the entire course of the War, such as the planet Forseti which appears in the Definitive Edition of “First Strike.” There were also several planets mentioned in The Fall of Reach which had been skipped by the Covenant as they made their way to Reach, but they were never named. No list of untouched planets has even been made but they do exist.
There are also planets which the UNSC successfully defended at one point, but it was never said if the Covenant eventually returned and glassed them or not. So they may or may not be prospering.