I am having the same issue. Here's what I discovered and, hopefully, I'm right AND it will soon be resolved.
When you start with a fresh download, everything works fine, but if you did a little deeper into the Analysis and Synthesis Messages you may find a string of lines that reads,
"Warning: Messages from megafunction that supports OpenCore Plus feature
"+ Warning: Messages from megafunction that supports OpenCore Plus feature Nios II Processor
" + Warning: The reset input will be asserted when the evaluation time expires
"Warning: Megafunction that supports OpenCore Plus feature will stop functioning in 1 hour after device is programmed"
After that hour, you can download your Quartus sof file, albiet, time limited. After the hour expores, you'll get
Using cable "ByteBlasterII [LPT1]", device 1, instance 0x00
Pausing target processor: not responding.
Resetting and trying again: FAILED
Leaving target processor paused
Eventually, if you keep recompiling Quartus, SOPC and NIOS IDE projects, you'll find you get an error relating to a mismatch in the read versus expected sysid and timestamp values.
If you get here...STOP...you're just spinning your wheels!
Call and submit an Altera mySupport SR! I certain it's license related
Chris