Hello @kovidgoyal
Sorry to report a little bug I have stumbled across.
When using the Tools>Add Cover, for some reason it deletes the first file.
Check this video where I first delete the existing cover.xhtml file, then use the tool to add a new one...
https://streamable.com/svebgh
edit...
And noticed that if there is an image file in that deleted file, it also deletes the image file.