Sane Update WIthout Losing Customization

Added plugins contents to /blog/user/themes/antimatter/templates/partials but each time Grav erase these additions to this file when updated.

Isn't there a way to keep custom changes when Grav updates?

any changes/custom settings to plugins are in:
usr/config/plugins
these settings are not touched by updates

Use theme inheritance. Do not update the existing plugin, but rather create a new one and add your twig edits in there.