In the most recent update to Ideate Explorer, you can choose to fix ALL Identical Instances by either Retaining Originals or Retaining Latest.
By default, the Retain Originals or Retain Latest will select ALL elements that contain the Identical Instances warning. In my example, there are 64 Curtain Wall Mullions and 11 Furniture items for a total of 75. Again, these 75 elements will either be original elements or latest elements based on the Revit ID Number.
In the image below, it shows a Cancel on the delete and then switching to the Explore tab with the Display set to Current Selection. This allows the ability to uncheck elements that you may want to retain for whatever reason. The example now shows ONLY Furniture selected. You can see that 22 items will be shown in the Explore tab, but only 11 are deleted based on the option of Retain Original or Retain Latest.