[DiapDealer]

It adds the backup image to the archive because Irfanview is creating new file in Sigil's scratch area. The same thing would happen if you manually copied a file into the the epub's working temp folder while the epub was open for editing. Everything there is included in the zip archive when you save the epub. It's not manifested because it's being added to the archive at the filesystem level rather than with Sigil's API. Same for your rename scenario. The file is being renamed at the filesystem level by Irfanview, so Sigil has no idea whatsoever that the manifest needs updated.

It's a shame Irfanview has no other options to work with, because I don't see any easy way to fix it on Sigil's end. Not without hard-coding an Irfanview-specific hack, anyway. The only other possible solution would be to scan for, and delete, any unmanifested files found after an OpenWith operation completes. And that just sounds like overkill to me. And that still wouldn't account for any renaming of files with an external editor.