Just to check, the problem is the "Charis SIL Modified" and "Charis SIL SmCp Modified" fonts appearing in the font dialog? If so, there is something wrong with how they are displayed. The names aren't displayed as the font. That suggests that the names are still in a list somewhere, but the font files are no longer there. What happens if you select one of those fonts and press OK? Or "Add font" or whatever it is to embed the font.
Do the fonts appear if you open a font selection dialog in another application? If they do, that suggests Windows is the culprit. If they don't, it points more to calibre.
I think the thing to do is scan the registry for these name and search through all the files in the calibre config directory as well. Another thing to do is to run calibre in debug mode and see if there are any errors when the font selection is opened.
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