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I checked the "Ignore mismatched system ID" and "Ignore mismatched system timestamp" in the System ID checks, but that didn't help.
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First, you shouldn't do that. This error means that there is mismatch between what is in the FPGA and what Eclipse is expecting. This shouldn't be ignored.
Try to redo those steps in that order:
[list][*]regenerate the QSys system[*]save the QSys design[*]recompile the Quartus project[*]Regenerate the BSP in Eclipse (using the clean option first if necessary)[*]recompile your software project[*]configure the FPGA with the .sof file you just recompiled in Quartus (be careful, if you have some IP in evaluation mode, the generated file will be called project_time_limited.sof instead of just project.sof)[*]download the software from Eclipse[/list]
and see if it works this time
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