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Yes that is expected behaviour and has been forever in Sigil.
I just rename the current file to a unique name, import your html file version, delete the old renamed version, then do a find and replace in html, toc, opf that fixes external links back from the unique name to the original name.
If I need to do this for more than one file, I just unzip the epub and drag and drop files.
Thanks!
I will merge this into my next posting!
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