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I was just about to ask a similar question but I searched for posts with "ligatures" first. I'm having the same problem with a PDF. Text looks fine in the PDF, I export it to a text file and each of the "bad" characters is exported as a period. When Calibre is used to convert it (and when one on-line converter I found is used) the following problems happen (there might be more combinations, but this is what I've found):
If "ll", second one missing. If "ff", both missing. If "tt", second one missing. If "fl", both missing.
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