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So, a js from a plugin is located in the header based on the setting below:

wp_register_script('plugin_min', plugin_url . 'scripts/scripts.min.js' );

Now, I can change it so that it will be located in the footer by editing the plugin file:

wp_register_script('plugin_min', plugin_url . 'scripts/scripts.min.js', array(), false, true );

Of course editing the plugin file is not a good idea since it will be overwritten upon update.

So, to do it properly, should I deregister it first then re-register in the function.php?

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Your thought is correct.

By editing the plugin file you lose updatability. So unregistering and reregistering it in the functions.php would be the correct way to do it.

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