How to overwrite modules by default with DRUSH?
Overwrite
Allows the project to be installed in a directory that is not empty. If not specified this is treated as FALSE, Drush make sets an error when the directory is not empty. If specified TRUE, Drush make will continue and use the existing directory. Useful when adding extra files and folders to existing folders in libraries or module extensions.

projects:
  myproject:
    overwrite: TRUE