Bootstrap.css changes to the minified version after applying a Bootswatch theme. If I revert back to the default theme, the bootstrap.css remains minified. I would prefer to work with the non-minified version.

Hello David,
This is how the extension is supposed to work - the bootswatch themes come with minified css files. All the changes you need to make should be stored in a separate css file, included after the bootswatch theme.