Repair of EP1C6 and 3064 based main board. Need help!

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If I understood you correctly, you want to set one of the Cyclone's pin low.

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Yes. This one of condition to start CPU boot clock I found comparing to good board.

Maybe there are many other conditions that I dont know about.

I will try this software from link you gave me.

But even if I will do it.. I'm not sure that other board components are good.. and I'm not sure Cyclone will be configured from flash.

So, still looking for the way of uploading .rbf file direct into Cyclone.

I need to eliminate every broken part of this board step by step.

It is realy hard.

At this time I'm sure that 3064 is programmed well.

Main CPU is replaced. ( try soldering 350 balls BGA chip at home :) )

Cyclone is replaced... and I stoped at this point.

"Blank" Cyclone is blocking other units to start.