Not sure what you are saying - that the convert is not inserting the cover or something else?
Calibre has never updated the copy of a cover embedded in a book that it is stored in its library. Normally the cover is updated on exporting a book from Calibre (either via Save to Disk or Send to Device) as long as the cover is clearly identified in the source book. The cover is not updated by these action sif the cover is not identified, or if the format does not support the concept of a cover (e.g. pdf), and in this case a conversion is necessary to embed the cover.
For epubs there is the new plugin available that allows the cover of an epub to be modified 'in situ' in the copy of the book that is actually in the calibre library.
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