Last night, while I was debugging a program (I am using microblaze) and doing some changes in C in SDK, my program stopped functioning.
My SPI stopped working. I cleaned up the project files, I even re-synthesized my microblaze and the design. Nothing. The thing is, that my other pins are working normally.
It is not easy to help with this kind pf issues, what version of ISE/EDK are you using? ISE/EDK prior to version 12 is highly unreliable and unpredictable.
The rule of thumb is NEVER re-synthesize your design when you are done with the HW design, keep a working project, archive it and then use that for designing your SW, this way you minimize the possible problems and can go back to the original design whenever necessary.