I don't know how relevant this is, but there is an old thread
here that discusses a quirk in the NOOK reader, not Kobo, whereby the cover isn't properly recognized unless the attributes of the "cover" meta tag appear in a certain order.
I mention it because one of the things Sigil
might do (even if all you do is open the epub and do a save-as) is re-arrange the order of attributes in the meta tags. Whereas I think it less likely that Sigil would rename the cover image file.
Another thing Sigil will do with a content.opf that comes from an InDesign export is clean up the formatting by adding newlines and tabs (i.e. "pretty-print") to make it more readable.