Yes, hand inputing incorrect paths will confuse the updating process. But if was broken beforehand it will not be magically fixed.
I always turn on showing full paths in BookBrowser as I like to hand input my paths and I need to understand where files really are.
I thought there was also a plugin that handled embedding fonts?
Update: There is ...
See Doitsu's CSSFromFonts plugin here:
https://www.mobileread.com/forums/sh...0&postcount=17
And since plugins may be new to you, here is the link for plugins for Sigil that are freely available:
https://www.mobileread.com/forums/sh...d.php?t=247431