If your just adding a cover there is a good chance calibre can add it without any additional work. Properly built EPUBs for instance can have their covers changed. In cases where it doesn't work an EPUB to EPUB conversation is necessary and this will have minimal changes as a result of conversion.
Changing the cover is really going to come down to the format of the ebook. MOBI for instance is a lot harder to change but it is still possible.
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