What happens after products are manually linked?

Right after the product is linked, Shopee / Lazada stock will be immediately updated to be the same as the Shopify inventory. If there are any differences between Shopify and Shopee / Lazada stock when the syncing begins, it will first be synchronized to Shopify stock to start. After that it will start synchronizing as normal.

For example: if "Product A" has 4 stock in Shopify and 3 stock in Shopee, it will reset to 4 stock to start. After that it stay in sync when either Shopee or Shopify has stock changes.

If you have variants sync, price sync, titles sync, description sync, images sync or SKU sync enabled, those will also start updating immediately. For example: if you have variants sync enabled and Shopify has 5 variants while Shopee has 3 variants, 2 more variants will be added to Shopee.