Due to a known problem in the Quartus® II software version 14.1, you may not be able to configure an Arria® 10 device over JTAG if there is also a MAX® 10 device in the same chain which is not being programmed in the same JTAG operation.
To avoid this problem, physically bypass the MAX 10 device on the board and only configure the Arria 10 device, or configure both devices in the same operation.
This problem is scheduled to be fixed in a future release of the Quartus II software.