Remove Nios referenced files from project no longer using Nios

Yeap! as inusual as it sounds.

by reading the warnings of the project I found that some say,

XXX file not found... and

some constraints ignored while trying to reach a instance of a component which is no longer in the design.

Update: I was able to remove many of them, by Project-->Organize Quartus Setting File.

Saving the project.. AND Closing Quartus completely... removing db and incremental_db

Reopening the project.

Recompile all.

However there still some references that still try to reach some old components.