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You've already broken the Number 1 rule of using Calibre. Don't mess with the files in the library folder. Let me repeat that. Don't mess with the files in the library folder.
Normally this would result in a lot of headaches and pain and a bit of swearing as you try to fix what you broke, but in this case you're in luck. You can still delete these books from the Calibre database, using the method you should have used in the first place.
Start the Calibre program. Filter your books for deletion (use "Formats" in the Tab browser to show only .mobi books). Select all the filtered books, then right-click on one of them and choose Remove -> Remove files of a specific format from books. Choose Mobi and press OK. This will remove the mobi formats from the books while preserving the epub formats. Normally this will also delete the mobi files from the library folder, but you already did that yourself. And yes, I tested it to make sure it won't get an error.
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