This warning means Shuttle did not copy the Etsy quantity to Shopify for this variant. Your Shopify stock was left as it is.
Why it happens
You turned on "Keep variants that continue selling in stock on Etsy". With that setting on, Shuttle skips the update from Etsy to Shopify for a variant when all of these are true:
Shopify tracks the variant's stock.
In Shopify, the variant is set to keep selling when its stock reaches zero.
The variant's stock at the Shopify location Shuttle uses is 0 or below.
If syncing from Shopify to Etsy is also on, Shuttle sends these variants a fixed quantity so they stay buyable on Etsy. That quantity is not real stock, so it is never copied back to Shopify. If that syncing is off, the setting only blocks the update to Shopify.
How to fix it
If syncing from Shopify to Etsy is on and you want these variants to stay buyable on Etsy, you need do nothing.
To sync these variants the normal way again:
Go to Settings > Stock Syncer > Shopify → Etsy.
If you cannot see the "Out of stock and negative stock" section, turn on "Enable syncing from Shopify to Etsy".
Turn off "Keep variants that continue selling in stock on Etsy".
If you turned on syncing in step 2 only to reach this setting, turn it off again.
Click Save.
To fix one variant, add stock at the location Shuttle uses in Shopify, or edit the variant in Shopify so it stops selling when out of stock.
To change the quantity Etsy shows for these variants, go to Settings > Products > Shopify → Etsy. In the Stock Quantity section, enter a number from 1 to 999 in "Default stock quantity", then click Save. Empty means 1.
Still seeing it?
Contact support if the warning continues after you turned the setting off and saved, or for a variant that has stock at the Shopify location Shuttle uses.