Hm, that doesnt sound right. I have always edited metadata before on DRM files (without drm'ing them) and reloaded them, and they were readable on the kindle they were downloaded for. That was a new calibre feature maybe six months ago? There must be something else going on. Are you sure those books were downloaded for your kindle?
I would also delete the 'whispernet files' before reloading them from calibre. The process I use is from Amazon, purchase the book for my kindle but first select 'download to PC' option. Then from calibre I add them to the calibre library, add a cover, metadata etc, and then load them to the kindle. I hate having multiple files.
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