If I need to upgrade a theme on a self-hosted Ghost instance, do I have to delete the theme first in the control panel and then upload the zip file or do I just upload the zip file and it overwrites the theme? I am using the Editorial theme.
Upload the zip and it will overwrite (you should get a confirmation dialog asking if that’s ok) 
Done, it says it overwrote buy now its listed twice. Thanks for the help.
You have a capital e on your active theme and lowercase e on the non-active. That could be why it’s listed twice, I’m guessing Ghost will read the capitalisation are two different themes.
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