You can’t do anything there, this is basically a bug in iOS.
The fact is that the iPhone mode on the iPad prescribes the iPhone 4 and saves the displays in general. So, here's how it is implemented: iPad just displays a 320x480 viewport. When you press the "2x" button, the viewport does not change. Things are still displayed at 320x480 and are (poorly) scaled.
Apple should definitely improve this and display your application in the retina when it is in 2x mode.
Do not invest more of your time, but only Apple can fix it.
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