"Retained" was clumsy; "rehired" would be better. All of the writers I listed were working as freelancers (except, perhaps, Roddenberry), which the series relied on heavily for stories.
Fontana signed a contract in February of 1968 to write three scripts for the third season (with an option for three additional scripts). "The Enterprise Incident," "Joanna," and "Survival" were all written for the third season as part of that contract. She hated the way all three were re-written and she declined to write further for the series.
Writing as Lee Cronin, for legal reasons outlined in the Solow/Justman book, Coon continued to work as a freelancer for the third season. Story outlines were turned in for "The Last Gunfight" and "Wink of an Eye" in March of 1968, and "Spock's Brain" in April of 1968. "Let That Be Your Last Battlefield" was a second try at a story that had been junked in the first season ("A Portrait in Black and White"), but Coon wrote a new story outline in March of 1968.
So, no, those weren't leftovers from season two's script development.