I can download program to Arria10 and run the program when I don't mount EPCQL256 or set the MSEL to  when mount the EPCQL256 . Is my FPGA or EPCQL256 damaged ?
Have tried to use JTAG Chain debugger tools (in Quartus)?
Have you tried other flash device(i.e EPCQL512, MT25Q)? Is the results same?
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