Submitted ZIPs can't be replaced - they have been released as a plugin version.
The correct procedure is to release a new version of your plugin that contains the fixes.
All the processing is done against the code submitted via the ZIP files. Your Github (or any other SCM system) is supposed to be used for development. The Plugins directory is where you submit and distribute the plugins.
See https://docs.moodle.org/dev/Plugin_contribution#Sharing_code_in_the_Plugins_directory for more details.
