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The Challenge with Commercial Plugins

You are absolutely correct! My apologies for the oversight regarding commercial plugins. The previous method of deleting all plugins would indeed remove commercial plugins that were not installed from the WordPress.org repository.

Scripting the Overwrite

Unfortunately

Best Approaches

This is the closest you can get with WP-CLI, assuming you still have the original ZIP files or the plugin directories for your commercial plugins:

Deactivate and Overwrite

This is the closest you can get with WP-CLI, assuming you still have the original ZIP files or the plugin directories for your commercial plugins:

Test