Originally Posted by saiyuki
I looked at the Duplicate Plug-in, but it gives no option to check duplicate filenames including the extentions - .epub, .mobi. Is there a way of achieving this either using the plug-in, or through Calibre itself so i am left with just EPUB's.
That's because the idea of a 'file name' does not exist within Calibre. Only the metadata database exists, and that's what the Find Duplicates plugins works on. So if your EPUBs and MOBIs are different formats of the same book according to Calibre, it's easy:
formats:epub and formats:mobi
as a search term will give you books that have both a MOBI and an EPUB format. Select them all and do a right mouse button -> Remove Books > Remove all formats from selected books, except... -> Pick EPUB.
If they are not the same book according to Calibre, you'll have to either merge them by hand or play with Find Duplicates.