I have done this by importing the cards (with all tagged with NEW), keeping duplicates, then doing some searches in the card browser to
- Find all duplicate notes and add duplicate tag (notes->find duplicates)
- Delete cards with tags duplicate+NEW (
tag:duplicate tag:NEW) - Reposition all new cards tagged either duplicate or NEW (
card:[card type] (tag:NEW or tag:duplicate) is:new) - Remove duplicate tag (
tag:duplicate)