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You can't call it an 'erroneous warning' - it's perfectly valid and simply draws you're attention to the possible issue. If you have a glitch on your clock or PSU that causes the PLL to lose lock then it may not recover without a reset.
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Are you saying I can't rely on the "PLL Auto Reset" set to On in the Settings tab of the altera_pll wizard? I see in my poorly worded post I did not make it clear that it seemed to me the warning about needing a manual reset should go away.
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If you have a mechanism whereby you can pulse the PLL reset in the event of the lock signal deactivating then you clearly should do so. If you don't then, as you say, you'll have to live with it. The question is how likely is the PLL to lose lock? Good question. However, if you have anything critical (in your mind) that can't cope with it losing lock then you need to design in a means of resetting it.
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I'm afraid I don't see any way of resetting it in our case. Hopefully, as long as the input clock is stable it won't lose lock but I'm a bit concerned about noise. About the best we could do is toggle power to the whole board if we lost communication with it.
Thanks for the help.