You are doing 2 different things.
The Spine is the Order of files in the book. But Why that way?
Simply drag the file in the book browser to its new place (order).
Record is the line in library view (it is more complicated than that as Calibre is really a full relational DB, but the lifting is done in the GUI/CLI)
Make the change, then embed (to force into the Library copy). Send to and Save to do this on the fly
for the Exported copies only