Your Etsy listing sold out, but Shuttle left the matching Shopify variant's stock as it was. That variant takes backorders and its stock is already below zero. Shuttle skips it on purpose, so your backorder count is not reset.
Why it happens
Shuttle skips the update when all three of these are true:
The Shopify variant is set to "Continue selling when out of stock". You can check this on the variant in Shopify.
The variant's Shopify stock is below zero. This usually means it has orders waiting to be filled.
The Etsy stock for that variation is 0 or lower.
The Negative stock handling setting does not change this. Shuttle skips these variants whichever option you choose.
How to fix it
If you want to keep taking backorders on Shopify, you do not need to do anything. This message is expected.
If you want Shopify to follow your Etsy stock again:
Restock the item on Etsy. Once the Etsy stock is above 0, Shuttle updates Shopify on the next sync.
If you do not want backorders for this variant, turn off "Continue selling when out of stock" for it in Shopify. Shuttle then updates the variant on the next sync from Etsy.
If you get a different negative stock message after you do this, Negative stock handling in Stock Syncer > Etsy → Shopify is holding the update. See Negative Shopify Stock Level Ignored or Handling Negative Stock When Syncing Quantities from Etsy to Shopify.
Still seeing it?
Contact support if you see this message for a variant that is not set to continue selling, if its Shopify stock is 0 or higher, or if the Etsy stock is above 0.