I have been struggling with my Flex two slice setup with WSJT-X, JTAlert, N1MM, and HRD. I have everything running except slice B (second copy of WSJT-X) is not flagged stations that have been worked before. The adif file is the same for both copies of WSJT.
I have attached a screen shot and you can see both slices are on 40m and the b copy is not catching the dupes. I use N1MM as a dupe checker while running as well. All contacts are pushed to HRD for final keeping and upload to LoTW, eQSL, ClubLOg, and QRZ.