Originally Posted by srascal
I tried converting using Calibre, but a large part of the CSS, namely font-faces and margin-left, were stripped out. I tried adjusting the settings on Mobi Output to say "both" or "new" for the mobi output type, but the resulting file did still not have the CSS properties when I tested the files onto my Kindle Fire.
If you know of a way to zip mobi files with KF8 formatting and media queries by using the command line or any kind of software, please let me know. Thanks
I think you are getting confused here. Mobi does not support embedded fonts. So that won;t carry over from an ePub > Mobi conversion. Also, when you use Kindlegen to convert from an ePub, you do keep any embedded fonts because Kindlegen creates a combined KF8/Mobi file and when you view this on a device that supports KF8 such as the Fire, you do get the embedded fonts as you are viewing the KF8 part.
If you want a version of your ePub for Kindles that also include the embedded fonts, use Calibre to convert to AZW3. That is KF8 and will keep the fonts and the margin formatting. Converting ePub to Mobi will only do so much depending on what features are used in thee ePub. There's nothing you can do about that other then to dumb down the ePub (not recommended at all).
You could have ePub, KF8 and Mobi versions of your eBook and go with that. But be advised that on eInk Kindles, there is a chance that the embedded fonts could possibly have line heights that are rather large. There's nothing you can do it in the coding to fix this. The only way to fix this is to edit the metrics of the fonts so they have a smaller line height.