After seeing the result, it looks like InDesign removes the ligature from the font, but keeps the information that there's a ligature... As far as I know, ADE will only render a ligature if it exists in the font, i.e., if it is defined there; so the font output by InDesign has the definition of the ligature, but the glyph is blank (which is a stupid bug, if you ask me). A possible workaround, if you somehow want to keep the mangled font, would be to include the explicit ligature characters somewhere in the book (possibly where they are not visible), hopefully that will force InDesign to include the ligatures in the mangled font, but you'd need to check all available ligatures.
ADE 1.7 probably works fine because it doesn't try to render ligatures at all.
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