How do you connect the products between Shopee and Shopify? Are you doing it with the product name or the SKU?
Shopee and Shopify each assign their own internal IDs to their products. The app knows which Shopee and Shopify product are the same is by linking them together by their internal IDs. When the product is published from the app we keep track of all the IDs and match it with Shopee and Shopify IDs. The product SKUs and names do not matter.
For example, for product "Red T Shirt". On Shopify the ID might be 11, the Shopee ID might be 5300. The app needs to link them together "Shopify ID 11" is linked to "Shopee ID 5300", then the app will create the Shopify order with the correct Shopify product. When there is a change in the product, the app will see that "Shopify ID 11", therefore it will change "Shopee ID 5300"
If you try to add a new Shopee product from Shopify using the app, the app will automatically link them.
But if you already have products on both Shopify and Shopee, you will need to manually link them with the app by following the instructions here: Manually linking existing Shopee products to existing Shopify products