I can't tell if I'm missing something or if Level 2 has a serious backtracking issue...
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I went clockwise around the right "gear", clearing 1S3E and 2S3E. (Obviously I'm going to have to clear the latter again if I want to get through here again, but that's why there are seeding beacons.)
I played around with 2S2E, said "ugh, nope, come back to it", and proceeded on to 2S1E. I said "cool, optional" and kept walking.
I went through the left gear, clearing...well, some of it, and said, OK, time to get back to the right gear. Now:
* I can't get back in through 2S1E; there's a green door at the north and unfriendly arrows at the west.
* I can go back through 3E. But when I do, there's no way to go south from 1S3E, because once you've cleared it there's nothing to weigh down the pressure plate to remove the arrows blocking passage south. Worse, you can't go back to 3E, because there's three yellow gates blocking progress.
So it looks like (a) you can get stuck in those rooms, which is not good, and (b) you can't backtrack to 2S2E if you don't clear 2S1E the first time through (which is very not good).
Am I missing something? Is this an error in the hold, or in my logic?