- Assuming the number of replacements you want to do at any given time is small, then why not drag/drop the replacement files from your editing location into the the Book Details panel of the relevant book.
I do it frequently for RTF, PDF, EPUB, MOBI & PRC formats - the new files replace the old files in the relevant "library/author/title (id)" directory. You can also drag/drop replacements into the Edit Metadata Formats box.
I found it by suck it and see, it doesn't seem to be documented - Managing book formats
has - "You can add a new format, delete an existing format and also ask calibre to set the metadata ..."
I hope its not a bug - I'd be lost without it