Yes, you can open regedit on windows (just type regedit in the start menu) and then navigate to the SketchUp version you are using and find it there. I suppose there is a similar approach on Mac but don’t know exactly how it’s done. I think you may need to restart SketchUp for it to forget these values.
You can also leave out the pref key until you have decided the sizing and positioning of the dialog and only then add a pref key. In some cases, e.g. if you want to mimic a dialog box you can also leave out the pref key completely as these typically don’t remember their position.
Use #set_size and #set_position to change an existing WebDialog or HtmlDialog. The values passed with the constructor are only the default values that will be used if there is nothing stored for the preference_key. Deleting the information itself associated with the preference_key cannot be done with the API.