The algorithm that I use in my
epubQTools (--myk-fix option) and I can confirm that it works in many many books prepared by this tool.
To avoid font stripping problem:
1) The
main font
must be set up for body tag.
2) The
main font
must not be used in other selectors
except above body tag.
3) Use
other fonts according your wishes
4) CSS style file with above styles
must be linked with every XHTML file in ebook.