And once again, you cannot pick and choose which metadata you pull from the book file. Not even in S&R. (Which never looks inside the files, on account of it is an S&R utility not a get-metadata-from-the-book utility.)
But if you got the metadata in order by filename, rather than by editing the metadata (like in calibre) then maybe you shouldn't have tried maintaining metadata in two locations.
Perhaps you could use a script to extract the comments metadata via ebook-meta.exe and modify the book record via calibredb.exe