Is the name "Afra" reprehensible? And did the Prophet, peace and blessings be upon him, change the name "Afra" to "Khadra" or "Afra" (meaning dust-colored or reddish-brown) to "Khadra" (meaning green)?

The default rule for names is permissibility, unless a text prohibits them. There is no text prohibiting the name "Afra'" (عفراء), and its meaning is: pure white. As for "Afrah" (عفرة), the Prophet, peace and blessings be upon him, changed it to "Khadra'" (خضرة), because "Afrah" describes barren land that does not produce vegetation, so he changed it as an optimistic gesture towards greenery and vegetation.