Sure, just open it and read/write whatever you want... I often add some LabVIEW keys to it, if e.g. the executable is named hello.exe I add:
[hello] HideRootWindow=True This way the window of the application will not have two entries on the start bar. You can use the configuration VIs to read and write keys to the file. The file will always have the same name as the executable. If you add a section called MyConfig and save e.g. a logging frequency to the file in addition to the LabVIEW keys it will look like this: [hello] HideRootWindow=True [MyConfig] LogFrequency=10
