On Windows SketchUp writes the state of the the tray dialogs to a Private Preferences.json which is in User/AppData/Local/SketchUp/… Some users have reported that this file doesn’t get updated when they save and repairing the installation (with Run as administrator) appears to allow Windows to grant permissions to SketchUp to write the file.
You could manually edit the .json file in a text editor and delete the tray related entities.
Save the edit. Then in SketchUp set the trays the way you want them and save the SketchUp file. If SketchUp can write to the file it will rewrite that information.