This works for me.
Scripted close of WindowViewer and batch file automatic startup of the second application.
a) In the InTouch installation directory C:\Program Files\Wonderware\InTouch right-click and select New->Text Document.
b) Give the text document the same name as your first application.
c) Open the text document and enter "ping -n X 127.0.0.1 > NUL" and "View "C:\path\to\your\intouch\app\"". X in this case is an integer of the number of pings you want to perform before Starting the specified InTouch application. I have tested X at around 20 which appears fine for a small application, I would recommend that you test this and change as appropriate for your system.
d) The ping item is used to delay running up the second application to allow first application to shutdown.
e) Save and exit editing the text file.
f) Change the file extension for this text file to .bat
g) Repeat the above steps to create a batch file for your second application.
h) In WindowMaker in your first application, add a button to a window with an action script animation.
i) On this script add use the WWControl function to close the application (see above).
j) On this script also use the WWDOSCommand function to run the batch file that starts the other application; WWDOSCommand("name of batch file", "INVISIBLE");
Conclusion: Using this method the operators will click the shutdown button in the active application and it will close, then after the delay specified in step c) later the second application will start.