The first thing to check when linking a Variant between TradeGecko and Shopify is to ensure that the Product Structure matches between Tradegecko and Shopify.
For example, in TradeGecko you have Product A with Variants 1,2,3 and Product B with Variants 4,5 but in Shopify you have Product A with Variants 1,2,3,4,5. In this case, you'll only be able to link Variants 1,2,3 from Product A between both platforms but NOT 4,5 from Product B on TradeGecko. This is because TradeGecko creates a link on the Parent Product (in this case Product A) and will not let Product B be linked to Product A as it is a separate product.
To resolve, you'll need to move the variants from Product B to Product A in TradeGecko to match Shopify's structure or separate the Variants in Shopify into two Products to match TradeGecko's structure and then link the product(s).