Originally Posted by koadic
The only problem I see in step 4, is that any special formatting for the book, regardless if you want to keep it or not, is then removed from the file never to be seen again unless you have a backup or another copy of the file you download. Sometimes there are elements that enhance the appearance of the book that it would be nice to keep, so it is cleaner to just modify it instead of removing all of it. But as far as xpgt files go, most of the time those are safe to remove, as they are only used by 'Digital Edition' readers anyway.
I personally don't use calibre to modify epub files, as there is very little in the way of fine control. I would instead suggest installing Sigil, and edit the epub files that way.
You have some good points to consider.
You might loose some of the special elements, but if you have your own css codes, this is usually not noticeable, at least for me since I have my formatting preferences set in my css. You can always try and leave the .css file, but since the OP is having troubles with the fonts not converting for them, the .css file is likely the culprit.
Sigil is definitely a more involved but controllable method for doing it. It also takes longer, and if you don't want to learn another learning curve, it may not be the best method for the OP. The only other problem I have with Sigil is that it is still very buggy imho, crashing while you are trying to work with it as well as being extremely slow software - often leaving you sitting there for upwards of 30 seconds while it is trying to do simple things like split your chapter into 2 new chapters.