Think of it this way: in your situation, the runner is still a runner whether he is on 2B, on 3B, or in between. During a live ball, he risks being put out, but he's still a runner. In your play he is not forced to advance, so he may return to 2B (as long as you judge that he's not "running the bases in reverse order" to "make a travesty of the game").
In contrast, when the batter hits a fair ball, he becomes a runner. As such, he may run back and forth between 1B and home (for example in a run-down). But once he passes the plate, he is no longer a runner and should be called out. No legitimate base running is possible at that point.
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Cheers,
mb
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