Theme update not overwrite to retain settings?

New to Shopify theme building and I quite enjoy doing it.

When updating the theme changes via CLI, it will overwrite the changed files for that theme and reset the data used in that theme. Is there a way I can update the theme that UPDATES the theme and keeps all of the previous settings?

So if I have theme v1, and I build v2, how do I go about uploading the v2 to replace the v1 but keep all the data.

Thanks