What platform are you on? It's possible to unzip and rezip in Windows. On a Mac, it requires a special utility or the Terminal command or the rezipping doesn't occur successfully.
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Try re-exporting and in the InDesign ePub Export Options Panel > Contents, unticking Include Embeddable Fonts.
Hi Derek, as I mentioned in the opening post I have done that and my epub looks fine and is using the same font that i chose, but are there any negatives to having unchecked the box?
If you don't want to included any embedded fonts make sure there is not a fonts folder included, delete any reference to the fonts that InDesign may have carried over to the content.opf file. Finally, open up the container.xml file. InDesign sometimes inserts font embedding in here. Delete any reference to fonts and you should pass epubchecker without any font warnings.