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The situation is about the same. Actually, with my method the text is not muddled, so I wonder why it is for you... Images and everything are retained (if you extract them from the ePUB of course...
Merging in Sigil is easy. Select the text files you need in the Bookbrowser, right-click and select merge. I usually then copy the new HTML file in Notepad++ for additional work. I don't save the ePUB, because I want to keep that.
Extracting the images and stylesheet I do with a zip-program. Yes, it is still manual work. BTW, either retain the file structure or adjust your links.
Changing the header is also easy. In you big HTML file, delete the first couple of lines. The first line must be <html>.
Copy the line I mentioned above between the <head></head> tags.
The stylenames will be gone. Blame Microsoft if you want.
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