You may reach out to eBay account customer support and request a limit increase.
For eBay account related seller questions please contact: 1 (866) 540-3229 or https://ocsnext.ebay.com/ocs/home
You are also able to lower the quantity per listing for eBay. Doing so will have no effect on your Shopify quantity.
Within sync settings in the channel, set up auto restock, so that when eBay quantity reaches a specified level, as long as that quantity level or more are available in Shopify, the software will auto restock eBay.
Then bulk edit your quantity for eBay within the sales channel to a lower value to free up some space in your limits so you're able to publish additional listings.
Here is how to bulk edit in the sales channel: https://support.connectebay.com/hc/en-us/articles/115002055911-Bulk-Edit-eBay-Listings