Swatches disappearing after save of product

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The situation, there is a WordPress 4.1.17 running with a custom theme.
It also has Woocommerce 2.3.7 and then the WooCommerce Variation Swatches and Photos 1.6.6 plugin, which has no section here.

We do an import with WP All Import and then the swatches are showing fine on the front-end. Yet after we save the product again these suddenly disappear.
It is not a front-end issue as a var dump shows the color before and not after the update.

Any ideas?