I had an expectation of how Calibre would work that resulted in me making some assumptions about the behavior I was seeing. For that I apologize.
The behavior I am seeing is that the .azw3 file created from the epub file has the changed description.
I haven't looked at the code for some time, (in my view it doesn't follow Robert Martin's clean code guidelines or the SOLID principles which makes it difficult to read and understand; and I shouldn't need to do so), but I seem to remember that it uses an intermediate form when converting from one format to another.
I never looked at how the metadata is handled, but I am assuming that the data used in the output file is coming from the Calbre database, and not the source file.
So I guess that is how and why the conversion happens.
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