Rather than using:
you can use:
axesHandle = findobj('Tag', 'tagForYourAxes');
plot(axesHandle,[1 2 3],[1 2 3])
...
axes(findobj('Tag', 'tagForYourAxes'));
Just change 'tagForYourAxes' to be whatever you set the figure's tag to be when you created the GUI with GUIDE and use that snippet . This should work, but I could not fully test it since I do not have the .fig file.
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