Sorry guys, I missed the "great refitting" and really just checked Game 5. I'm not using my PC that often anymore, which is why this happened in the first place...
As for the flak issue: At least the (as of yet unpublished) version 0.15 of the game's manual states that flak hits ships without phase shielding moving to or through a flak hex. So you shouldn't get hit leaving a flak hex - if that was your question. (Just once if your movement ends on a flak hex, or you're passing one during movement phase.)
Somehow I got logged out of the forum, I kept checking it, but seeing no new posts. After two months, this got me suspicious, and I realized they were dated far more recently than I had thought. logging in, suddenly it lit up again.
Well, clearly that's a rule misunderstanding on my part. As of now, *leaving* a flak square is at no risk to you.
Ironduke, the follow up to this is, when a flak is fired at a ship, does it immediately try to hit the ship? At the moment, that doesn't seem to be working (but I think I had tried to code it). If this answer is
no, then you would never want to fire flak directly at a ship, since it would only leave the flak square. If the answer is
yes then I need to look into why they aren't trying to hit upon "arrival" in a hex.