If you’ve already found an answer to this that works well for you, I encourage you to post it here for others to see. If not, the way I would go about it would be to use a custom filter or an action.
Where the menu is output in the theme, either use apply_filters or do_action to trigger the override you want, and in your plugin, hook into that action/filter to output the override. This is a more non-destructive way of accomplishing the same task, as you then don’t overwrite a menu association.
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