I downloaded the active theme from ghost and just added an error-404.hbs file to the theme. The 404 page works but when I refresh the home page it changed from a magazine style to just a long list of posts that have small pictures. Also, the return home button did not go to the home page but to /page/2.
I doubt the error page is actually to blame. Instead, I’d evaluate whether maybe you have settings to adjust in /ghost > settings > design & branding > theme tab. When you upload a theme file with a different name, your settings get reset to the default. That sounds like what might be happening here.
Thank you that is good to know, that sound exactly like what the problem would be.
Cool. Hopefully you can figure out which setting gets you back to how it was before you uploaded. At worst, activate the old theme for a moment and see what settings are present there, then switch back and duplicate them. :)