Custom loop in addition to default on archive page

I’m with s_ha_dum that this isn’t very clear on what’s happening, but have you tried wp_reset_postdata()? I believe you would put it before the last while loop in your example above.

Here’s an article on other methods of resetting the query if that’s not working: http://digwp.com/2011/09/3-ways-to-reset-the-wordpress-loop/

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