Can I keep track of which rows have been merged?

Yes, you can track which rows have been merged so that on your next merge it will only merge new rows.

From the Google Docs Add-on

Just create a column and name it whatever you want. Say ‘Merged’. Then click the Options button from the Sidebar 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.

From the Google Sheets Add-on

When emails are being merged, the add-on will automatically enter the date and time of the merge in the Filter Rows to Merge column. This column is automatically created for you when you try to create a merge for that sheet. To merge these rows again you need to clear/delete the date/time values in the Filter Rows to Merge column.