I have a site collection that is having issues with its style library library. I had 2 css sheets stored in there that mysteriously disappeared. No matter what I do, I can't list the files - powershell and the om both are unable to find it. However, when you try to upload a document with that name it errors out and tells you it can't rename to that because that file name already exists. Is there any way to remove this entry? Or is the best route to just recreate the site collection?
What happens when you view the document library using the Open with Explorer functionality? Do you see the files there?
You need to make sure you file's type attribute is set to GhostableInLibrary
This article provides a good walk-through for deploying branding solutions even if you do not use Sandbox solutions.