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What do you mean you copied it?
It sounds like you are jumping in and out of Sigil. Sigil imposes its own structure on epubs. There is no choice about it. If you alter the structure you are likely to blow up the document.
If you want something that will work with other programs you have and does not care about structure, use the calibre editor.
Sigil is built around error checking to make sure the epub is valid at all times. It is the basis upon which Sigil is constructed.
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