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Also, #2 not a big issue if you load template ePub first and only load non-template files from old ePub. This is even easier if you preface your template ePub files with names indicating their source (preface filenames with template or temp or std or ...).
Replacing multiple possibly linked in html can result in lost footnotes, orphan images, orphan multi-media. Using global rename on the old ePub in Sigil before merging should also work.
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