There isn't a "Make Current Value Default" method that you can invoke programmatically, this would require your VI to be saved when it was closed, which obviously couldn't be done if it had been built into an executable.
You could read the values from the controls/indicators and save them in a .ini file using the Configuration File VIs on the File I/O palette, and have some code at the start of your program that reads the values from the file and puts them into the objects using local variables.