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Since you only flashed the fpgaimage, you must have used the newer version software. As such you must flash all three sections bootrom, fpgaimage and osimage at least once as their location in the memory has changed. After that you can only flash one section at a time.
What you've done now, assuming you were using the original ebuller firmware, is to overwrite part of osimage with fpgaimage thus corrupting the firmware. Reflash all three parts and you'll be OK or go back to the ebuller firmware.
There is a version of code that lets you flash either as you please. The FPGA image is still loaded by the main OS code, this has nothing to do with flashing the ARM.