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Generally speaking conversion works pretty well. The issue is that epub uses current html standards, while mobi is using a bastardized version of html 3.2. This means that there could be things in the epub that don't convert well to mobi.
The most common issue is margins - Mobi doesn't really support them except through nesting blockquotes, and the Kindle handles this more poorly than pre-Kindle generation mobi renderers. What that means is for a lot of epubs you need to disable margins completely (a Calibre option on mobi output), and indented blocks of text will probably become un-indented if they just used margins/padding. I've generally switched to using blockquotes in my epubs in case someone converts it to mobi down the road, but not all epub creators do this.
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