I think what is happening is that because you set the windows appearance properties in the main VI and not in the subVI itself, the app builder used the default setting for the subVI and removed it's front panel. You can change this in the application builder by going to the VI Settings tab, slect the subVI, and click the Edit Build Settings button. Change the Remove Panel to No and all should be okay. You can also change the subVI's properties itself (VI Properties>Window Appearance>Customize) and not have to change anything in the app builder.