Remove Deleted Items
You will notice that when you remove items from the website, those items will remain in the PIM, but will be highlighted red. If you are sure that you are not going to re-enable those for the web at a later date, you can remove them from the PIM database.
To remove an individual deleted item, or a group of deleted items, simply select the appropriate items, right-click and select "Remove Deleted Items".
To remove all deleted items for the PIM, simply enter the "Edit" menu in the top left corner and select "Purge Deleted Items".
This will remove ALL of the deleted items and ALL of their associated PIM data (Web Descriptions, etc.) from the PIM. Be absolutely sure this is what you want to do before performing this action.