why did Herr Otto Flick leave for the last 6 episodes of series 9

Flick did not leave the series, it was just a different actor. Flick supposedly had plastic surgery to alter his features. I don't know if it was planned that way, or Richard Gibson had a reason to leave the show at that time.

Richard Gibson wanted to move on and unfortunately nobody knew after the 8th series that they would only do one more. I'd imagine if he had he'd have carried on.

A damn shame because he couldn't be replaced.