From my recollection, it should allow SAM-BA to work, all things being equal. I'd have to dig out my 9261-EK board to experiment.
However, let me reiterate that SAM-BA, the PC application, is not very robust. It tends to fail when you'd most like it to work properly.
This is the document for the 9260-EK, the entire 9xxx range work in a fairly similar fashion, so insight you can draw from it is applicable to your board.
http://atmel.com/dyn/resources/prod_doc ... oc6281.pdfGeneral advice.
Provide traps doors in your flash based code that permits the device to be erased. Look at how the 9260EK AT91BootStrap uses BP4 to erase the boot blocks in Nand or Data Flash devices.
Provide a means to break, or go into a monitor mode, on the serial port.
Provide a means to enter RomBOOT/SAM-BA mode from you boot strap code.
Test and debug code when it is running in SRAM or SDRAM before burning it into FLASH.