Retaining unused logic with Quartus?

The Quartus setting on the help page copied below should take care of the outputs that don't drive anything.

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Preserve Fan-out Free Register Node logic option

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This option can be set in the Assignment Editor.

A logic option that specifies that the register should be preserved in the design even when it becomes fan-out free.

This option is available for supported device (Arria GX, Cyclone II, Cyclone III, HardCopy, MAX II, Stratix II, Stratix III, and Stratix IV) families.

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