New starting in 4.4.1 we'll be adding a code changes file for manual upgrades. This way theme changes will not be lost. The change file will only be available for upgrades that don't have many changes. Major change releases will still require a new install. We do hope however for the most part this new feature will be used more frequently than not as we don't expect major code upgrades to happen very frequently.
Please note code change files will require you to manually update templates or the custom.css file manually.