AFAIK, these ligatures are primarily created by OS X apps on a Mac and will usually only be displayed correctly if the eReader fonts support them.
If the fonts installed on your eReader do support them and you still see question marks, the only way to fix this is to globally search and replace either the characters or the entity definitions (e.g. fl for fl) in the original source files, before converting them to another format with Calibre.
Since the lines are from a commercial ebook, you may want to contact the book seller for more support.
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