The handle structure for GUI created with GUIDE are stored in the figure object for the main GUI menu.
gui1fig = open('FirstGui.fig');
gui2fig = open('SecondGui.fig');
Then if the first GUI needs to reference a handle that exists in the second GUI,
handles2 = getappdata(gui2fig);
and access handles2.TheHandleName
If need be, the second handles structure can be updated from the first GUI by using
setappdata(gui2fig, handles2)