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Message is generated during Publishing. This message is usually followed by one or more additional messages, including Document XXXX/manifest.mfx' has never been checked in. The server copy cannot be published..
There may be many reasons for this. Check the document mentioned in the Path column of the ActivityLog, and locate this in the Library. If you cannot locate it in the Library, check the Deleted Documents view. If the document is there (but is not linked to anything (if it was, you'd also see Broken links messages, then the problem may be that the deleted document was previously included in the published Outline but was removed and deleted, but somehow the Incremental publishing thinks that it is still a part of the outline and can't find it. The only way I have found of resolving this is to delete the entire publishing destination folder, and then re-publish from scratch again.