After you create the plot that you do want to draw on to, use gca() to get the handle of the plot axis. Record that, and when you want to use line() to plot to that same axis, put the recorded axis number in as the first argument to line().
For example,
plot(rand(1,10));
handles.plotaxis = gca;
guidata(gcf, handles);
Then later,
handles = guidata(gcf);
line(handles.plotaxis, 1:10, exp(0:.1:1));
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