The mass merge tool uses the global delete process towards the end if you wish.  I worry that there is a slight risk here (although we have very clear procedures) of deleting the wrong records.  also is there a chance that someone could import onto or input onto a record which is then deleted between it being merged and the deletion taking place?  the 'old' plugin gave you the option of deleting as you go along (my understanding is that it would delete as you merge immediately).  I preferred this way as I felt it was much less risky, but there may be a good reason why this wasn't put into the functionality of the new tool?