I was not aware that CC doesn't open the zip file. As you say, that likely points back to code in Calibre instead. I have a couple metadata plugboards that are applied that I've used for years, but no metadata modifying plugins.
I'm not able to find anything about manually testing the wireless device interface. Can I get a pointer or a phrase to google for that? Pointing my browser at ipaddr:9090 gets some basic library metadata in JSON after a lengthy (~5minute) wait.
I am assuming (possibly wrongly) that the 'smart device' AKA wireless device interface is different than the Content Server.
I also noticed that the corrupted zip files were ~2x the size of the correct one.
Of course, now I can't duplicate the problem even sending the same file from Calibre. So that helps a lot. And now I can't find any other cases of it, just to insure I look crazy.
Until I can duplicate the problem again, it's basically impossible to troubleshoot. So I'll go away again for now.
Thanks for your help, folks.