@JSWolf - well to be fair to Barb-B, she doesn't really care what epubcheck says, she just wants to be open the book in Sigil after doing a metadata update without having the opf corrupted. It was you that asked her to try the epubcheck route
Thanks for the reply Kovid. Given you have checked the spec and what calibre generates is correct, then that would appear to only leave Sigil as the culprit. I will drop an email to the other (i.e. active) Sigil devs and see what they have to say about it. Certainly since I see the exact same behaviour from a simple Save to Disk operation from calibre I don't feel there is anything that needs to be changed in the Modify ePub plugin concerning it.