You may know that M2E Pro allows handling your existing Channel inventory using the Unmanaged Listings functionality.
To manage Items imported from the Channel, they need to be matched with Magento Products via automatic or manual linking; and then moved to the M2E Pro Listing.
Once the Item is moved, you can change the Magento Product it is linked to. For this, switch the M2E Pro Listing grid to the Settings View Mode and apply the Link to another Magento Product action near the necessary Item.
Once applied, in the opened window you will be able to link your Item to the relevant Magento Product.