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The image you show is not a good filter; the ferrite bead should have capacitors on either side to create a pi-filter
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There are more capacitors connected as DE nano schematic shows.
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My question is; how important is the isolation filter between VCCINT and VCCD and how should it be designed?
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Referring to your first question, not all Altera DevKits have a filter for VCCD_PLL, some are simply tying it VCCINT. Others are even using a separate analog voltage regulator for it.
VCCA is the most critical supply node related to PLL operation, because it's supplying the VCO. PLL stability problems have been considerably reduced since Altera introduced a FPGA internal voltage regulator for the analog PLL supply. According to my experience, VCCD isn't critical for a standard PLL application not chasing for minimum PLL jitter. In so far, a common supply for VCCINT and VCCD can be acceptable with good bypassing.
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