I just faced with the issue yesterday that I created my own search configuration to store only one field value in the index. I thought that it’s enough if I only index that one field what I want, but NOT.
So if you have something like this, then you will have duplicated entries in the index, because when you change the item and save/publish Lucene doesn’t know that you have already this in Index and it should be updated. So it creates a totally new entry with a different “_uniqueId”.
If you add the “_uniqueid” also to your config then Lucene can update the entry, and you can get rid of the duplicated entries.