Can't ECO modify PLL's properties of Cyclone V devices?

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The PLLs on the Cyclone V don't work the same as the earlier parts. Read the PLL chapter of the device handbook. Since you didn't give any details on what you were trying, I can't say why it doesn't work.

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I want to modify the PLL's output's phase after full compilation, so i used to use ECO to modify it. Which makes me implemented it fast whitout full complie my project again.