Bugs in NIOS II EDS.

I had the same problem. I found that a file in my backup drive named ".altera.quartus" had files paths that pointed to a directory of a previous installation of Quartus. When I deleted that file, everything worked fine. I would recommend that you do a search for the ".altera.quartus" file and view the contents to see if it contains the same file path as is listed in your error message. If so, try renaming the file and try to load the build tools again.