I added the .cue to the zip file, I explicitly have the fix options set to Test, Rename Files, Rename Rom, and Remove Zip comments, Don't want it to remove Useless files, roms, find missing roms or creating dummies. After I add the .cue file, I explicitly tell it to remove Useless roms from the advanced menu, to cleanup the old .gdi file from where I added the new .cue to match the Redump Dat.
Instead it goes off and starts doing the following:
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Create new file Cool Boarders Burrrn! (Japan).zip Rippin' Riders (USA).zip : Move rom Rippin' Riders (USA) (Track 04).bin to Cool Boarders Burrrn! (Japan).zip/Cool Boarders Burrrn! (Japan) (Track 04).bin
Not the behavior I'd expect when I have specific options enabled/disabled in the general fix settings, and I told it to explicitly do one operation (remove Useless Roms).