Dan,
Is there a similar example on YouTube or elsewhere that you can share, to give a better idea of just what you're going for? I follow you all the way up until you refer to changing pitches.
But generally speaking, it seems to me that patching together multiple clips may be the only way (using the step sequencer at least, as it's a pretty uniform tool within each clip). Either that, or you
might be able to do it with just one big single-beat (as in SS beat) clip that contains the total number of steps (musical beats) in the whole measure (e.g. 15), then construct the whole measure, including the skipped step part. That will give you one full clip, complete with the skip, that you can duplicate and repeat over and over, if that's what you need. You may or may not need to play around with your tempo setting using this method though, to get it to play at the desired speed.
Let me know if we're making any progress toward your goal.