Can you explain a bit more about this? The tool is intended to reconcile transactions that you manually add using the Tiller Money Labs add-on that are flagged as reconcile so that when the automated feed brings them in they don’t get counted twice. If you were trying to use this for managing duplicates because of removing and then re-adding an account it makes sense that it didn’t work for you and you had to manually manage the duplicates.
There’s a separate Manage Duplicates workflow in the Labs add-on.