I don't know about the Bookerly font, but for a font to work properly on a Kobo device, the internal font name and the name of the file should be identical. Open the font in a font editor and check for full font name. If your font file is called Whatever-Regular.ttf, then the internal font name should be Whatever-Regular as well.
If the font names are identical and it still doesn't work, I have no idea what to do. So far, whenever I had an issue with a font on my Kobo that was the problem.
ETA after reading Geoff's post above: I only use regular epubs, never kepubs, so I can't say anything about them.
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