Executive Meddling: Oddly, in the favor of the show. The first 11 episodes are generally considered the worst part of the franchise, with none of the characters being particularly interesting or sympathetic. Then the studio replaced the writer at the time with Tow Ubukata, upon which point everything from the characters to dialogue to world-building were massively improved. It was praised enough that Ubukata has been in charge of writing everything (except for the short-lived manga) Fafner-related since.
Considering the release dates, the 2nd season of Strike Witches was likely recorded around the same time as the Fafner movie, and Stephanie Sheh plays a main character in Strike Witches, so that's probably why they were able to bring Sheh back. Also, Sheh was credited as Jennifer Sekiguchi for that dub, and JYB as "Kevin Hatcher".