Copying a site to an existing site without using the incremental or delta options will result in duplication of the items in lists. And, copying a list to an existing list will also result in adding every item from the source list to the target list.
Libraries enforce uniqueness using the file names. When the Incremental Copy option is selected, any duplicate items in the target will be replaced with the source item.
Lists (unlike Libraries) enforce uniqueness through an internal attribute (item id). This attribute is automatically generated and sequenced by SharePoint and cannot be overwritten. Therefore, a different approach is used to identify new and updated items, but the result is the same as for Libraries. Any duplicate items will be deleted from the target and then copied from the source item.
Essentials does not preserve Item ID, and, to have a way to determine uniqueness for items, we set a property on all migrated items to determine the source item for the purpose of identifying which items from a source correspond to the items in the target. Checking for this property takes time on a migration and doing so is not a default behavior.
The Incremental copy option has a filter that allows for the determination of the number and age of the changes that will be brought over during the incremental copy. By selecting the number of days, weeks, or months, you can choose to only bring over differences from the last full copy that were made in the determined time.
If selecting "0" as the value for the incremental filter, the tool will do a content analysis of both source and target and bring over any content that is identified as differential. In the case of this migration, if a file exists in the source that is not in the target, said file will be copied to the target. In the event that the item exists in the target, the tool will check to see if the item in the source is newer than the one in the target (based off of last modified date). If so, the item will be deleted from the target and copied from the source to the target.
In order for an incremental or delta copy to function correctly on lists, the items in the target must have been moved from the source using Essentials. If they were put into the target by any other means, they will not be compared to the items in the source and items will duplicate even if they are the same item, since name is not unique in lists.