This is why it's generally recommended to mark things as inactive instead of deleting them (unless you know they've been unused long enough as to not have any other references hanging around in the non-historical indexes).
The easiest way to get rid of the errors is to re-add the item and mark it inactive. You will also want to confirm that everyone has the setting to 'show active records only' checked on in their item grid configurations.
An alternate method for accomplishing what's desired with deletion is to use the toolkit to combine all items marked for deletion into one item which is kept but never used for any other purpose.
Otherwise I think you are stuck ignoring the DIC errors relating to the items that have been deleted, or removing the offending lines with GVRW.