I inherited a site that was already customized in Sharepoint and Sharepoint Designer. I was asked this morning to revert the entire site (plus sub-sites) back the default theme and I can't get it to apply correctly to all the sites. When I go to Site Settings, Site theme and apply the default site, it does not apply to the customized sites.
There are a couple things to take a look at as far as the site theme.
Check to see if you have a feature running on your sites that is enforcing the use of the custom theme. We use a feature that applies the theme and some other customizations to our sites and prevents sub-site administrators from going off on their own customization tangents.
It is also possible, although not recommended, that the customized theme was made by modifying the default theme. If you are lucky you will be able to use SharePoint Designer to revert back to the orignal version of the file, or they were wise enough to copy the original default theme to another file in the themes library so you can just copy it over to the default theme file and get things back to default.
Lastly, they may have edited or replaced the core.css file instead of creating a unique one for the theme. Again, check to see if you can revert versions if this is the case or if someone kept a copy of the original around.
And the lesson here is never fool with your default theme or core.css files without having a backup of the files. And better practice is to never fool with them at all. Name your themes and css files differently. :)