Can I keep track of which rows have been merged?

Yes. Just create a column and name it whatever you want. Say ‘Merged’. Then open the Options dialog and set the ‘Merged’ column in the ‘Track Merged Rows’ field. This will allow the add-on to write the date/time that row was successfully merged. To avoid merging rows which have already been merged set the ‘Merge Specific Rows’ to the ‘Merged’ field as well. This will make the add-on skip rows with any text in the 'Merged' field.