Here is what happened to me yesterday:
I wanted to edit a book to improve its format but thought I should make a backup in case I wrecked the file. The easiest way for me to do that from within Calibre was to convert the epub (without making any changes) so that an original_epub file would be created. After backing up the book I used the Open With (Sigil) add-in and spent the next hour reformatting my book. After saving my book in Sigil, I closed Sigil and checked that it still opened in Calibre. So far all was fantastic...but I noticed a typo in the metadata. I corrected the typo and reconverted the book to incorporate the metadata change into the book. OOPS.
I forgot that Calibre always converts from original_epub to epub. Because I had made a backup original_epub Calibre used that as the source of the conversion and over-wrote my epub file.
My hour of edits was lost.
This has happened to me before when making search/replace regular expression edits with the Calibre conversion tool itself. It is not possible to make incremental search/replace modifications without deleting the original_epub file between conversions (danger of losing everything).
Would it be possible to configure Calibre to always use the epub file as the source of any conversion. That way Sigil or Regular Expression Search/Replaces would be incremental.
Would it be possible to always replace the original_epub file with a numerically index file so that multiple copies (at various stages of edit) could be kept. e.g. When converting title.epub the original file becomes title.1.original_epub. When title.epub is converted again the latest title.epub becomes title.2.original_epub etc.