This issue is usually caused by a Matrix Parent product being set to "Sell on WebStore" prior to assigning it to a matrix.
Matrix Parent and Child products should be created and staged prior to setting any of the products to "Sell on WebStore".
To resolve this issue, enter the Title of the product in Shopify into the Delete Tool at accumula.com to remove it from Shopify. So long as "Sell on WebStore" is enabled on the product cards in LightSpeed, these products can then be updated by opening the product cards, unchecking current, rechecking current, and saving the product card. The products will be synced to Shopify on the next sync cycle.