Downloading ELF process failed "how to remove unconstrained paths"

Might have been signals moving around in the symbol. SOPC Builder used to do that a lot but I'm not sure about Qsys since I haven't used schematic entry for a while. To check for that rightclick the background of your schematic and click on "refresh schematic" or whatever it's called (I don't have Quartus installed and I forget what the option is called). That'll update all the symbols in your design in case any of them changed.

Also if you didn't already constrain the JTAG I/O I recommend doing so. If you look at any Nios II design example that targets Cyclone III or up there should be a constraints file that has some for the JTAG I/O. It would take a while to explain why they are needed so take my word for it :) The LEDs and pushbuttons are asynchronous so you can cut those paths.