Your old book did not have the cover properly defined. That requires 2 things to be flagged (semantics) in the OPF.
1)the image file (the name IS NOT the flag)
2)the (x)HTML file that uses the image AS the cover. (this file can NOT also be flagged as something else. Covers are seperate)
Using the Add cover tool does the flagging.
BUT (to your other problem)
Calibre Library only
AUTOMATICALLY sets the cover SHOWN on ADD, not from a BOOK edit.
If you had opened the Metadata editor: Selected the format on the right: then click the brown book Icon (gets cover from format): OK
That forces a fresh cover to be used for the library.
there is also an Icon for metadata.
Also note that Updating the Library metadata does not AUTOMATICALLY update the LIBRARY COPY of the book. (Books sent to devices by calibre, update on the fly, leaving the Library copy, pristine). To force the LIBRARY copy to update, you need to use one of the embedding tools like
Polish