Whenever I update my theme to a new version, it resets the customization options of the Design & Branding page in my Settings. Actually, more specifically, the Brand tab settings are preserved, but the Theme tab settings get reset.
I am using version 5.109.1
Database type MySQL 8
I am hosting Ghost through Magic Pages.
Theme settings are theme-specific because each theme can define what those settings are.
If you upload a theme with the same name (folder name+package.json) then it will be treated as an overwrite/new version of the same theme and the theme settings will be preserved. If you’re doing that via the Admin interface you’ll see a modal asking you to confirm overwrite of the live theme.