Hi,
I run the "at91sam9260ek_demo_linux_nandflash.bat" file and upload the "bootloader", "kernel" and "rfs" to the NAND flash.
Then I restart my board, but when I want to working with SAM-BA, the USB/ARM0 not detected.
But if I disable the NANDcs (or disconnect this pin from microcontroller) and restart the board, the SAM-BA will detect the USB/ARM0.
Has any idea for this problem or idea for solving it?

This is because RomBOOT is executing the code you uploaded to NAND, in order for it to enter SAM-BA it must not find bootable code as it searches through boot devices.

The 9260-EK implemented a software breakout mode in the AT91BootStrap where pressing BP4 erased the first block of NAND allowing for RomBOOT to enter SAM-BA mode when the board is nexted booted.

You should also be able to acheive NAND erasure using the uBoot command line.