there are no issues with "Upload a new version" it just doesn't work for every updates, and i rarely ask customers to install it as a new theme, so you dont need to be worry about this, even if i asked to install it as a new theme, you can simply install it as a new one without deleting the old one, so you can simply open both of the theme settings and copy paste colors...etc
-You do not lose any saved changes you have made, your custom colors and other settings will remain as it is after using "upload a new version"
-i do not suggest using custom.css, as i have explained above you can simple install the new version as a new one and then opening both of the theme editing in new tabs so you can simple copy paste your settings, it wont take 5 minutes and much more easier and cleaner, anyways, you never lose any setting changes you make unless you delete the theme.
Thank you
I'm glad you like it