When you run the GCS from a command prompt with a -help option it says this:
Usage: librepilot-gcs [OPTION]... [FILE]...
Options:
-help Display this help
-version Display application version
-no-splash Don't display splash screen
-log <file> Log to specified file
-client Attempt to connect to already running instance
-D <key>=<value> Permanently set a user setting, e.g: -D General/OverrideLanguage=de
-reset Reset user settings to factory defaults.
-config-file <file> Specify alternate factory defaults settings file (used with -reset)
-exit-after-config Exit after manipulating configuration settings
-noload <plugin> Do not load <plugin>
So just run it with -reset from command line.
There is also File->GCSImportExportSettings->ResetConfig. I think that also does what you ask.
I think you can also do it by zeroing all the System->Settings->SystemSettings->GUIConfigData