For correct synchronization of the product data between the Channel and Magento, you need to associate the Unmanaged Items imported from the Channel with the related Magento Store Views.
A related Store View, which you choose, will serve as a source of the Magento Product data whenever you are linking the Unmanaged Item to Magento Product.
To set up related Store Views in M2E Pro, navigate to your Account settings: eBay/Amazon/Walmart Integration > Configuration > Accounts > Unmanaged Listings > Related Store Views.
As for eBay integration, you will be able to choose the appropriate Magento Store View for each eBay site.
For Amazon and Walmart, you need to select Magento Store View that will be associated with the Marketplace set for the current Account.