Can I safely ignore these hierarchy connectivity warnings?

Thank you for the prompt answer Tricky.

I have investigated but I can not determine if these signals are needed or not. They don't appear anywhere in the source code. I know these output signals are missing from the cpu (nios ii gen 2) instance because the Connectivity Warning appears related to this instance and also in the RTL viewer I can find several signals with name A_ci_multi.... coming out of the nios ii instance. As the warning messages say the missing signals will appear in the entity code for the nios ii cpu, but this code is encripted.

I also can not find any reference to these signals in any documentation so I think I have reached as far as I can for myself. I think the only thing left to do is ask Altera support directly.