Help needed! can I connect cycloneIII's GNDA with digital ground?

The said isolated analog ground recommendation can be found e. g. in cyclone iii device family pin connection guidelines. AN466 - Cyclone III Design Guidelines tells in contrast

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GNDA and GND pins should be connected to the same ground plane as

the device’s digital ground.

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It seems to me, that the first recommendation is continuing an outdated concept found in some previous Altera design guides. More generally, I think that the concept of separated analog ground planes has shown inadequate in many mixed signal designs even with parts as high speed ADC, for various reasons. To mention just one serious problem: It tends to cause nasty ground differential noise voltages already at moderate distances (e. g. 1") from the common ground location. If more than one mixed signal device is connected to both planes, it's advantages are questionable. It looks good in data sheets and application notes dealing with a single device.

There have been other recommendations in the past, e. g. to have ferrites or decoupling resistors in both the VCCA and GNDA supply and a capacitor across the pins. With Cyclone III, the problem addressed with these measures - noise susceptibility of VCO supply - has become less dramatic due to the internal voltage regulators. Thus I think the AN466 guideline quoted above is more appropriate.