[KevinH]

Does the cover image show up as missing in Preview? You might want to go back and reload the MR page and re-read my answer to your initial query. I have expanded it as I think you are mixing adding xml comments to the opf, with adding xhtml comments. Mend only impacts the xhtml files not the OPF. No comments are allowed or saved in the OPF, so commenting out in the spine of the OPF is the same as deleting it.

I just tried what you did on my machine by commenting out the cover (the first entry in the spine), and it was promptly removed from the spine. But the Cover.xhtml file still exists in BookBrowser and the cover image still existed in Images.

So I can not recreate what you are seeing and I have no idea how that image got deleted in your epub as mine was still used and linked after doing the exact same thing. You must have taken or used additional commands, but without those I cannot recreate things to help.