Yes "cover.xhtml" it is no longer used for templates. Now cover-template2.xhtml (for epub2) and cover-template3.xhtml (for epub3) are what are used to hold the template information and they should be placed in the Sigil Preferences Location folder.
The file name created in BookBrowser will still default to be called "cover.xhtml" unless that name is already used.
Thanks!
Kevin
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