I ran into the same issue back then when I did my testing, but didn't pay much attention to it - I had all sorts of issues with the Quartus 15 programmer under Linux so I mostly used Quartus 14.
He seems to have had some problem programming the POF file from Quartus 15, and had to rebuild the whole project. If anybody else runs into similar issues, could they let me know, so I can figure out what might be wrong?
When I tried to open the .pof file with GUI Quartus Programmer 15 under Linux I got a crash notification. IIRC the command line quartus_pgm from Quartus 15 gave an error about an unsupported format or chip (sorry, can't remember exactly).
Opening the POF with Quartus 14 worked fine, and IIRC the SOF worked both with Quartus 14 and 15.
I guess it's best if you do a quick test with Quartus 15 yourself, it could well be that my issues were Linux specific.