
What I would suggest you do is go into the Documents\CoffeeCup Software and delete the Themes folder and simply re-install. After you do that, there will only be 4 folders (Default Layouts, HTML5 Layouts, My Themes and Themes). Everything you need is there.
If you are migrating from 12.0 to 12.5, the new version will uninstall the previous version but will leave the documents folder alone. This will give you a blending of the old and new theme structure. That is ok.

The new version also has an improved installer so that it can be installed under a limited user account. Before we could not do that with the Visual Editor. So depending on your configuration, you may have files from the old version in one location and files from the new version in another. Unfortunately we couldn't do much about that.
So my word of advice, when in doubt, just delete it and re-install the software.
