I think I understand what you have been doing, which on the face of it sounds confusing.
Making a copy of your original theme is good practice, as this ensures that you always have an original to fall back on.
Renaming your copied theme, is OK too, as long as you change the config.php doc, making sure that you declare which styles sheets you want to use as default style sheets for this new theme.
Making a duplicate copy of your new theme, and then renaming it is OK again, provided that you make the necessary changes to the config.php (if you have to that is). This is especally true if you have changed any of the stylesheet names.
Provided you have done all the right things, like checking that all the stylesheets are there in your newly named theme's folder as they should be, and your new theme folder is in the themes folder which is in your moodle folder, I can't see a problem.
What I don't realy understand is why the 2nd copy of the theme reverts back to Standard stylesheet. That is a real mystery. Perhaps someone might shine some light on it?
Mary at confused.com!!!