So now that Silent Bob has had a chance to wake up and read the blogs (failing to mention Media Morgue, I might add) and realized the whole geek nation was talking about his axing of the director role, he saw fit to put his two cents into the deal on his own blog to tell his side of the story.
To sum up his slightly long-winded, albeit detailed explanation as to why he would not be directing one of the episodes: it really was a scheduling conflict, stemming from the fact that Smith over-thought the idea to the point that they had to schedule someone else for the job:
The moral of the story, kids? You snooze, you lose. Or, rather, if you spend too much time overthinking a simple yes or no question, the guy who directed "The Last Seduction" will get your job.
Read the full explanation here.