You can store the handle(s) to the plotted objects somewhere in your app structure, and delete them and replace them with new plotted objects as needed.
% store the first plotted line as line_1
line_1 = plot(1:10);
hold on
% store the second plotted line as line_2
line_2 = plot(2:11);
% delete line_2
delete(line_2);
% make another line_2 with different data
line_2 = plot(3:12);
line_1 and line_2 here would be stored in your app structure, and they might be created and deleted in different functions within your application.
