A)
Further to Oleksandr's 1a = XPS procedure, you can have a look at this picture:
http://forums.xilinx.com/t5/Embedded-Development-Tools/can-sdk-elf-and-bit-download-FPGA-together/td-p/202393The file system.bit, created after hardware generation, is an uninitialized bitstream and does not include the ELF file. It is only when you execute the command to download or update the bitstream that the system.bit and ELF files merge into download.bit.
The download.bit file generated is a merge of system.bit and blinkLED.elf. The blinkLED.elf is (converted and) loaded into FPGA's BRAM using data2mem (automatically called in this procedure).
You should use Xilinx iMPACT to transform download.bit into download.mcs to write into the SPI Flash (as you have already done before).
B)
Further to Oleksandr's 1b = SDK procedure "SDK / Program Fpga menu":
"
1b) If you prefer to use SDK:
Each time when you download project to board by JTAG, SDK created download.bit file in hardware platform folder.
This file can be used to create MCS and it contains program in BRAM."
You should select
B*1) the correct system.bit file
B*2) the correct system_bd.bmm file
B*3) your blinkLED.elf file
The generated download.bit file is a merge of system.bit and blinkLED.elf. The blinkLED.elf is (converted and) loaded into FPGA's BRAM using data2mem (automatically called when you click <Program FPGA>).
I assume that you have already performed correctly these steps, but it is better to double check.
To be safer, you could try to create a new SDK project (if the current one may have become corrupted), copy your C code and be sure that your C project uses your BSP project and your HW project. You should also check your link script.
In the new (or in the old) project, you should check the following:
B#1)
Select your project in SDK.
Click Project > Properties
Select Project References
Both Hardware and BSP project should be checked
B#2)
Select your BSP in SDK
Click Project > Properties
Select Project References
Hardware project should be checked.
B#3)
point 2 recommended by Oleksandr in « Reply #3 on: Today at 11:20:13 AM »
Check that the BRAM is selected in the link script, not the DDR RAM.
Generate a new link script if necessary.
C)
About "SDK/ Program Flash menu".
It shows "No usable flash memory controllers were found in the hardware system".
TE modules use an SPI Flash. SDK only support BPI Flash. You cannot use SDK to program an SPI Flash, you shall use Xilinx iMPACT.