calibre is not going to generate a valid epub 2 file from an epub 3 source. The only guarantee that calibre makes is that if you feed it a valid epub 2 it will output a valid epub 2.
I dont know of any automated solution that will get you valid epub 2 from epub 3. I would suggest you contact the developers of the epub creating program and tell them to output epub 2 in the first place.
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