We have an issue with the ebay syn on Shopify
Shopify Listing items and stock not synchronize with ebay store
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Considering submitting a request with Shopify’s eBay App developers. Mention to them specifically the product you are having issues synchronizing and they should be able to look into the logs.
https://connectebay.zendesk.com/hc/en-us
From my experience so far they respond relatively quickly. So just send them a message.