This is a unique situation that sometimes occurs when products are removed from your online store, and still, show up in the Webgility product catalog under the online product list. In order to remove these (Store deleted) items from Webgility Desktop App, the store items data in Webgility needs to be refreshed.
The following steps will help to resolve this issue:
1: Navigate to Advanced Settings by following Integrations > Stores > Advanced Settings.
2. Under Application navigate to the Last download date for Store Items, Click the Clear button, Save the settings, and close.
3: Next you will need to download the latest product data in Webgility from the product catalog by going to Products >> All Product (under online store) >> Refresh button.
This process may take several minutes to get completed. Once it is completed,
A dialog box will appear with the confirmation message.
Once this product download is complete, the products removed from your online store will also be removed from Webgility.
Note: This applies to online stores except for marketplaces such as Amazon, eBay, etc.