This is a bug in the handling of deleted properties in the UI. If the property was of type "item", the UI will also show the referenced item as "Deleted item" also if it still exists. The correct behavior would be to just show the property as "Deleted property" and show the label of the referenced item as usual.
Version: unspecified
Severity: normal
Try this in your JS console:
$.evalJSON( mw.config.get( 'wbUsedEntities' ) )
This will not include the item used in the Snak using the deleted property. This is bad and a backend issue: The ReferencedEntitiesFinder::findClaimLinks does not (anymore?) find the item used in the Snak with the deleted property.
Also see EntityView::registerJsConfigVars, line 745:
$usedEntityIds = $refFinder->findClaimLinks( $entity->getClaims() );