I can't check that with CK as that CK has this lovely ability to crash constantly, even if I open it and go walk away from the PC for 15 minutes, it will be sat there with the error up about it crashing.
However, searching through F4Edit shows that all of the "EncWorkshopNPC" and "WorkshopNPC<sex>" have the Protected Flag.
But I am going to do a test again as I found what I think Huskaron was on about with that "Base Data" and removed it from UNPC, as it looks like I was looking at the wrong options.
This could explain why Named Settlers where surviving (Nikolai up at Tenpines for example) and the others weren't.
EDIT: I don't know what I have done, but all settlers are now spawning without names, and I can't even speak to them.