I think the issue here boils down to the cover function fletcher.hide. In your second example, using #diagram($A$, pause, $&B$), the behavior is normal if you comment out cover: fletcher.hide. So, as far as I understand, you would have a solution if you can switch between hide and fletcher.hide as your cover functions, as necessary. I had a question on this topic a few days ago, and the only thing I could figure out was to use a state that would switch between cover functions. It’s not a pretty solution, but if you need something to work you might try that.
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