Could you tell me please how to rewrite the program of the microcontroller on the SAM9-L9260 development board using SAM-BA and USB connection?
The procedure is described in the manual under "Restoring the default bootloader and kernel" on page 19. These instructions were made with old version of SAMBA called "AT91-ISP" but the steps should be quite similar if using newer version.
What type of loading I should choose in SAM-BA - NandFlash? What scipt - Enable NandFlash?
Yes, NandFlash option. Try the different scripts.