- Do you run your apps in the same instance of MATLAB?
If yes, set tags, or unique names for your apps in Component Browser, under UIFigure - Identifiers, and get their handles this way:
app1 = get(findall(0, 'Tag', 'AppUIFigure1'), 'RunningAppInstance');
app2 = get(findall(0, 'Tag', 'AppUIFigure2'), 'RunningAppInstance');
This way, you have access to both apps.
If no, I wouldn't know how to find the other running MATLAB instance.
- What about simplifying your problem into having a single app with two windows?
Note: don't use global variables, it's unnecessary.