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I set up the following through the Assignment Editor, but it didn't prevent the removal:
set_instance_assignment -name PRESERVE_FANOUT_FREE_NODE ON -to "test_block:stub"
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I don't know if it's a bug in Quartus, but I've also seen cases where no assigment or attribute would prevent a fanout-free register to be removed.
But note that you should use the "noprune" attribute. Otherwise, according to the manul, it could be removed early before synthesis. But that didn't help to me in some cases.
It was using the Web free version that doesn't support virtual pins. So the only solution for me was to either tap it with Signal-Tap (but then, it is not fanout free anymore), or using WYSIWYG primitives in a VQM file.
If you try the latter, note that Quartus makes a big difference between VQM and plain Verilog files. What makes the difference is not the file extension, you need to tell Quartus is a VQM file. You might also need to disable fitter WYSIWYG optimizations.
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