Nios Error

hello,

i wonder why when i download the the compiled nios cpu in the nios apex board, then i run a .srec file on it ...a statement will appear and ask me to press the reset button to begin download..but when i press it ..nothing would appear....

Then moment when i press reset, the board will restore its own configuration rite ? it would be no point since my configured nios cpu has a custom logic on it..