For integration with your website, counterpoint requires the use of a unique ID for all items. This UID must be in the Website SKU field and is what is used for the integration to recognize the item and update each item for price and inventory.
When the integration receives product data from CP it checks to see if that UID exists on the site and if so, will not create a new product but use the existing one.
If it does not find the UID, it will create a new product with that UID as the SKU.
With new integrations that involve existing products on the site that have SKU values that differ from the required CP UID, you will have to change the existing SKUs to the UID.
You can export a report from the CP integrator interface to provide you with a CSV file with the UID for each variation.
From The Modern Retail Integrator Dashboard you can click on the Functions Tab and Choose "Export Gridded Items to CSV"
At the next screen , press Start to begin the down load of the CSV file.