Compiling a multiwindow app as a web app

Before I start, I'd like to clarify that I am aware that you can't have multiple windows in web apps. I just have questions on how the compiler will respond and my current workflow prevents me from testing it out myself for awhile. Any help is appreciated.

At the moment, my app is only used on desktop. I currently have a couple of extra interfaces for advanced use cases that only I will use and will only need to run through the full Matlab environment. That being said, the rest of the app (aka the main window) is used by multiple people in my organization.

I'm considering deploying the main app as a web app so my users can access it more easily, but I still want the ability to use multiple windows for myself on desktop. I also want to only have 1 version of the app with simple variable to lock off the tools that only I need. When trying to compile a multi-window app as a web app, will the compiler prevent me from doing so? Or will it compile the app and only throw errors when a user tries to open one of the additional windows?