If a product is part of a variable product but you want to be a single you need to consider the implications on the systems.
Firstly get the product right in Retail Express, set the Manufacturer SKU (or Custom3) and make sure the Size and Colour is set up correctly.
Then you may need to delete the product in WooCommerce and contact us for a refresh.
You may be able to removed it as variable and change it to a simple product but you MUST let us know to do a refresh.
The other solution is to turn off the integration, update the two systems SKU's and then once both systems are update turn it back on re-loading both systems.
Update the SKUs in REX to the new values, the integration would then try to create these new products in eCommerce. You can then move the images and descriptions over to the new product and delete the old one. The integration will now be linked to the newly created product.
Products can still remain linked between Retail Express and your eCommerce store and not be available from your store front. You can unpublish the product from your store front during these changes to ensure they are not bought in error.
Similar constraints apply when changing the Manufacturer SKU, the system will be trying to update based upon the original settings.