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I think the different resolution is a red herring, it seems basically time-series plotting (in tseries/plotting.py) generally doesn't play well with secondary axes.
This is an example with no resampling that has the same behavior:
The second plot call overwrites the x_lim, probably because (internal details of tseries/plotting) _get_xlim(ax.get_lines()) only references the current axis, and secondary_y creates a second axis object (via twinx()), and the two axes aren't considered together. This doesn't happen with a non-timeseries plot, e.g. if you change the indices to [1, 2, 3, 4] and [5, 6, 7, 8], though I'm not sure why.
As the xlim changes, the original data is not visible any more.
Could be related to #2185
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