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Actually, they will not help with updating the opf. It is treated just like any file by FolderIn and FolderOut.
The easiest workaround is to use Sigil's RegexRenamer functionality to rename the files to be deleted so that once sorted they will appear as a contiguous block in BookBrowser where they can easily be block selected and deleted.
I will think about adding a menu item to Select Files by regex to a future version, although a plugin could handle this easily as well.
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