Maybe I am missing something here, but that just all sounds rather horrible?
You have a library which has the correct metadata, correct?
Why not either (a) Just drop your "new" ePub into that library replacing the old one (either drag/drop into book details panel or edit metadata screen formats panel) and then run Modify ePub to get the internal ePub metadata up to date (an optional step).
Or (b) if you want to keep a copy of your original epubs, just copy the whole library to a new library, remove all the book formats (using the Remove menu) and then just do the same step in (a) of drag/dropping in the new ePub,
or (c) create the second library as blank, then as you create each new epub version you use "Copy to Library" on the right-click menu to copy the book/metadata across and then do (a) above. This option means your "new" library only has books you have converted.
Fiddling with calibre's opf files and restoring library etc all sounds very nasty and you really shouldn't go spelunking in calibre's library folders like that.
Using Sigil to just edit the ePubs "in place" is by far the easiest approach of all (particularly when done with the Open With plugin) and is certainly the approach that most senior calibre users like myself do. Going to text files and thereby losing all your formatting and various other stuff before going back to ePub sounds a bit mad, unless the books are the most woeful of pdf conversions. But hey, whatver method you are happy with
