Why do I see missing signals on my NCO or FFT cores when migrating to Arria 10?

Due to a problem in the Quartus® II software, you will encounter port signal changes when you migrate a non-Arria® 10 (e.g. Stratix® V) FFT or NCO MegaWizard® core to Arria 10. 

Specifically the ports are changed to those used in a Qsys® system instead of those used in an IP Catalog® component.  See the "Avalon-ST Signals" table in the user guide and note the signals with "In Qsys systems" in the description field.

This is due to a problem in Quartus II software.

To workaround this behavior, open the Arria 10 component (NCO or FFT), select View>System Contents, right click on the core (NCO or FFT), select Set Design Environment>NATIVE.