Hi @konradh, I added the two flutes in NPPE, using Add instrument: one from Cinematic Studio Woodwinds, and another from Iconica Sketch (I switched both to One staff, not sure if this is needed, but it seems the right thing to do). Then on an empty Project I loaded one flute in Dorico Setup and, writing some notes and playing back, Dorico used the CSW for flute 1, then I added another flute, and, writing some notes and playing back, Dorico used IS for flute 2:
NPPE setup:
Setup in Dorico:
Note performer mixer showing the two flutes by NPPE (white frame):
Playback example:
Try it out, and see the results, with your libraries. Maybe start with a simple new project with only the flutes, as I describe.
@Christian_R, Once again, you know everything! Thank you. 
I will see if I can make it work with BBCSO and VSL. This trick would be good for many things.
I use BBCSO for 2nd violins because my VSL library (Synchron Special Edition) doesn’t have separate Violin II samples and I get phase cancellation if the 1st and 2nds play the same note in VSL. I don’t remember how I initially set that up unless NPPE just defaults to separate libraries for Vln I and I.
You are very welcome, @konradh
I know this problem 
Re-reading the NPPE manual (page 86-88), it seems indeed that setting the desired instruments to One staff, it will use the first flute instrument for flute 1 and the second flute instrument for flute 2, as I experienced:
Here the manual PDF for NP4 (NPPE section starts on page 78):
