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Not sure what could could result in an empty file. I would have expected a new populated one to be created if you used the Save button from the GUI. Deleting it should mean a new one is created the next time you run the GUI and save the settings. Note that the name could be something other than profile.xml if you have used the option to save a new profile.
The name of the current profile in use should be shown in the GUI on the right hand side just above the parameter tabs, and that will be the name of the .xml file being used (it should also be mentioned in the log).
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