I suspect that your phono preamp has an intermittent problem. I would suggest that you have it checked by a dependable technician. There's also a remote possibility that one of the connecting wires of your cartridge is not properly secured.
I'm somewhat inclined to agree with you. However dropping out on two audio channels at once takes an awful lot of explaining.
Obviously it is not his preamp.
He needs to connect something else to the CD input like a CD player using the analog outputs. Then we will all know for sure if this is a receiver problem or a turntable problem.
So overall because it is both channels I think I suspect the receiver more. So if it is the receiver, I suspect it may on the contact less switching circuit in the receiver. The are flip flop type circuits. All it takes is for one component to be out of spec. and the circuit will not stabilize properly and then you get this intermittent switching.
So I would advise the OP to see if it the turntable or the receiver and reset it if it seems to be the receiver.
One other thing that occurs to me is that this could still be an HDMI issue. On Marantz units the digital inputs and analog inputs are shared. But HDMI has priority.
So you have to have no HDMI signal going in, and if there is then it switches away from the analog input right away. So it is possible that the HDMI board, or something connecting to it, is creating an intermittent signal the is shutting down the analog input for brief periods. We know this is happening on both phono and CD input.
So I think the causes are either the switching circuits, the HDMI board, or the turntable.
If the turntable is excluded I would advise a hard reset to factory defaults. If not successful then repeat 3 or 4 times. If that does not resolve it then return the unit.
As I write this, I'm actually inclined to blame the HDMI board, if for no other reason than the fact they tend to be built in trouble units.