We are using the Github integration for our live themes. Each live theme has it’s own Github branch (live/store-name). We do the development work on another branch and push to a branch called “Release”. The Github workflow triggers when something is pushed to the “Release” branch. From there, that workflow pushes all the code changes excluding the setting files to all the other “live/store-name” branches. As we have the Github Integration set up, it then updates all the code on Shopify (without overwriting the settings files!).
Hope this helps.