Nios II CPU with debug module not detected

Seems a bit strange but I hope this helps:

Have you been saving old copies of .ptf files and just renaming them for example to keep as a backup?

The solution to my problem seemed to be not to have any copies of .ptf files hanging around in the design directory, other than the one I want. Even if I renamed a copied file the IDE seemed to get confused by the presence of another .ptf, so change .ptf to .ptftemp or something - it all miraculously got better afterwards.

As a general principle I now apply this to .ptf, .sof and .sopcinfo files because getting these mixed up and using the wrong copy leads to all sorts of chaos.