If for some reason a character used in the PDF cannot be converted it will be substituted with either a space or a tilde. There is now a feature called Characters Editor that when enabled allows you to control the characters that get substituted for missing characters or glyphs. While this may take you a bit more time up front, the end result is far superior than having to deal with spaces and tildes (~) throughout a converted file.
You can view the Characters Editor Manual for more details.
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