Just today I have run into a strange problem, in SharePoint Designer my folder "Style Library", which holds the css files for my site, is empty. When I navigate to it through "All Files" it is still there, but it has nothing inside it.
However if I open my master page and follow the css hyperlink in the code there I get to the file no problem and it even shows the correct file path to reach it. But again if I click on the "Style Library" part of the file path the folder shows no items and says its empty. I am 100% positive that the files were there yesterday as I looked into it to check a few things.
We are using SharePoint 2010 Enterprise edition, and the css file for the master page is not the only file inside the folder.