Wiesi,
I thought this was an interesting question, because I noticed a number of people with previous questions who had serious difficulty with .rtm files and executables, and they weren't even trying to add or remove menu items dynamically. Are you using .rtm files to define your custom menus both in the development envuronment and in the EXE?
If so, I think I agree with Dennis and suggest that you abandon that approach and just build your menu programmatically, as shown in the example he points out. That way, you can create an arbitrary menu each time the VI or EXE is run. One wrinkle is that you now have to create some extra logic for constructing, saving, and loading your run-time menus. I put together an example (attached, LV 7.0) that demonstrates one way to go about it. I tested both in the development environment and after creating an EXE, and it works fine.
I'm interested in something else: how do you plan to make your EXE flexible enough to actually respond correctly to newly-introduced menu items? I guess you'll have to take some kind of a "plug-in" approach, where the anticipated menu choices will lead to the execution of additional code that you are packaging alongside the executable?
Regards,
John