After

fig, (ax1, ax2) = plt.subplots(2, sharex=True, sharey=True)
ax1.plot([1, 2]); ax2.plot([1, 2])
ax1.twinx().plot([2, 1]); ax2.twinx().plot([2, 1])

zooming/panning one of the subplots only affects the other subplot along the x axis, but not the y axis -- because zooming/panning affects the twinned subplots, which only share their x axis, whereas the y sharing is lost (of course, it cannot always be shared with the original subplots -- the sharing needs to occur directly between the twinned subplots).

Having thought approximately 30s about the issue, I believe an easy way out would be to support passing an explicit share{y,x} argument to twin{x,y} (for the "other" axis, as the twinned axis is already shared with the original subplot, of course), so that one can properly re-link the twinned subplots between themselves.