I am not an expert but I think the only way is one at a time.
I don't know about you but when I went through this I found that while the sources appeared to be the same, there were minor difference that I considered important, A mass merge would have lost that information.
I started with FTM Version 16, and had put qualifying in formation in some places I should not have. Without going into the source record and moving those parts to other places they would have been lost.
While it was true for the sources, to illustrate, I will use a place. In location I may have put the correct information but in the description field I may have put a comment that had nothing to do with the place and was a comment on the person themselves. ie name may have been Joe not George.
I went through each source and place and cleaned up the references. It was a big task but my data base is better today for doing it.