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Thanks, I went over the settings but missed it!
What I have done, is:
I have RAW+JPG enabled to be handled together.
As Fuji Raw Studio creates .FP2 for RAF files and .FP3 for JPG files, I entered "RAF+FP2 jpg+FP3" at additional extensions (though the manual says only RAWext, I need to set jpg too).
 
Example listing:
DSCF9454.FP2
DSCF9454.RAF
DSCF9454(1).FP3
DSCF9454(1).jpg
DSCF9454(2).FP3
DSCF9454(2).jpg
 
 
This works, except that the (1) and (2) files are getting unique numbers during renaming. That is a different issue, which I guess is not possible to solve?
To get like, NAME_0001.RAF and NAME_0001(1).jpg instead of NAME_0001.RAF/FP2 and NAME_0002.jpg/FP3