Try telling a continuity-heavy story when a majority of the comic's material was created by someone else. It's like making a big sandwich, only to find out that most of your ingredients are off-limits due to your strict diet, leaving you with only lettuce and two slices of bread. Do you give up? Or are you still peckish for something?
I'm not going to bother trying to phrase my response using the food analogy.
Flynn was well aware last year that the Penders characters were being contested. Rather than quietly phasing them out of the story so that their loss would have minimal impact should the worst happen, he opted to make them more important, putting Elias in charge of a team featuring at least one other Penders character, having Naugus possess Geoffrey, and creating an arc focused on the echidnas. He gambled heavily on Penders losing the case, only to have things backfire at a very inopportune time.
If sufficient precautionary measures had been taken, the court case would not have completely disrupted the storyline. Controversy would have been lessened, and it's possible that Sega's scrutiny would not have been drawn, in turn preventing the reboot and new set of mandates (Freedom Fighter redesigns, lack of Mobius, etc.).