I've been having this problem for a while also. Certainly while using versions 0.7.#.
Before I discovered that Sigil can link a CSS file to the HTML files, I was writing the link style sheets code manually & I thought that I was making a mistake here. However it continued to happen after I found the Link Styles sheets option on the context menu.
For me the code in the CSS is deleted when I Save the epub before linking the CSS to one or more HTML files or without opening it and it happens even if I've used a style in the code. If I have the CSS file open when I perform a Save or Save as then the code is still there then the save has been completed.
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