On the inability to delete a custom theme, make sure you don't have the theme you're trying to delete mapped to a page. Custom mapped themes will not be deletable until you remove the mapping. As for the default.ftl issue. I had a similar issue a while back, where I made changes to the default.ftl that broke the code. I deleted the default.ftl in my theme only to notice the old theme was in place. The solution is to add /decorator/default/default.ftl back to your custom theme. When you do so it will bring in the original file. Save this and try to view your site again.
For some reason JIVE doesn't always overwrite a .ftl to it's default if it's simply been deleted. I hope this helps either or both of your cases.
Aaron J. Perrotte