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I modified the example project from CycloneIII starter kit cd. The project runs well except the system timestamp is missing.
Expected system ID: 0x8888 Connected system ID: 0x8888 Expected system timestamp: Not found Connected system ID: 0x8888Link Copied
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As You've regenerated the SOPC/QSYS file, You have to regenerate the BSP file also.
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Alternatively, you can just ignore the timestamp check in the 'Nios II hardware configuration' window.
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