You'd have to cross reference with Active Listings not Unsold. You can use eBay's File exchange to download a CSV of your Active Listings and cross reference with the CSV from Sku Grid...(save a copy of the CSV from sku grid in case you need to restore the data)
Just take the item ids from the eBay Active Listings CSV and paste under the reprice_sku column in Sku Grid which are your ebay item ids.
Then sort the Sku Grid CSV by the reprice_sku Column (basically to line up identical ebay item ids one on top of the other).
Anything appearing twice (a full entry with all info and one blank entry with just an ebay id entered) would mean that the item exists both on your eBay account as an active listing and in Sku Grid as being monitored).
Anything appearing only once as just a full sku grid entry with all info filled in would mean that it's in Sku Grid and not on eBay anymore. Delete those rows.
Any items that are appearing only once with no additional info other than the reprice sku (ebay item id) would mean that the item is active in ebay but you don't have it being monitored in Sku Grid. If you have any of those rows delete them as well. You'd be able to cover that by doing an Import from Marketplace later.
Once you're done removing unnecessary rows from the CSV. Save it. Please be sure you're not using Excel as it will mess up your ebay item ids -- use Google Sheets or Libre Office for free.
Then go to Sku Grid and Purge All Items (that's under Advanced).
Then go to Import/Export --> Import CSV and upload the newly saved CSV. Your entries that went to old listings would have been removed at that point.
If you had any items that were active in your ebay account that were not being monitored by Sku Grid, then at that point you can do an Import from Marketplace to pull in items where the ebay item id does not exist as the reprice sku in sku grid.
Those newly imported items would be paused by default, allowing you time to update the supplier URLs and unpause the items.
If you do not have any items that were not actively being monitored in Sku Grid, then you can disregard the import from marketplace part.