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There is another flow that isn't documented that could result in the behavior you are reporting, if you are using that flow I recommend sticking to the normal flow that SOPC Builder used as well (generate the files then compile).
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I am not even sure what that means (another flow). I had a working QII 10.1sp1 project with an .sopc file based design. I updated my tools to QII 11.0 and opened the project, let QSYS upgrade it, etc.
I did not do anything that I am aware of that tells Quartus to do 'some other flow' undocumented or otherwise.
But thanks, you have given me some hope and plenty of homework!
-dave
Honored Contributor
