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I assume you mean Calibre's metadata jacket, added using Calibre's Polish feature.
When I merge 2 epubs with Calibre metadata jackets in them, the jacket pages are included.
The jacket pages do not appear in the table of contents(TOC) because Calibre does not put the jacket pages in the TOC of the individual epubs.
By default, EpubMerge creates a nested TOC. Each source epub is at the top level and you need to expand them to see the individual book TOCs.
I would need to see the epubs you are merging to help more than that.
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