eBay imposes limitations on changing variations on existing listings, especially if the listing has had any sales.
Shopify Marketplace Connect automatically responds to errors when revising the listing by dynamically editing variations if possible, or leaving them in place but disabled / out of stock if not. This prevents listings from ending and relisting, which protects your sales history.
Please refer to this article for Revising and Relisting with Variations.
For further assistance, please reach out to email@example.com