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As I've never seen the encryption.xml file for fonts as I don't use obfuscated fonts, my guess for those is because it's already "hidden" the fonts, that's the encryption for the obfuscation.
Regarding upgrading internals, having done it multiple times myself: As for html to xhtml, upgrading the internals does not automatically rename files. That's a manual process. All upgrading the internals does is upgrade the coding and adding the nav.xhtml and other arbitrary files, literally that's all it does. There is no actual renaming of files involved.
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