I want two masters working together for my mod project: WAC.esm and my own master called CNRP.esm. However there are some duplicate items from WAC's realswords that I want to remove from CNRP.esm.
Any suggestions on how I might be able to do this...?

TES Edit?

I tried it with TES Edit, but I dont know what settings to use to get that effect. "Identical to master" doesnt work for two masters I dont think.

Tes4edit Identical to Master will only work when one esp / esm is master to another. In the scenario you describe, you'll have to search out the duplicates manually.
And if you haven't realized or don't know, your esp will need both WAC.esm and CNRP.esm as masters if you use the items in WAC you delete from CNRP.