Idle and Fault behavior are programmable on the PF700.
The 20-COMM-D interface in the PowerFlex drives can be configured to react separately to Communications Idle and Communications Fault events.
What's happening in your case is that the 1747-SDN goes into "idle" mode when you download a new program to the controller, and if you cycle power to the PLC obviously communications stops totally, resulting in a communications fault from the drive's persepective.
The exact parameter number depends on your version of the drive, but look in RSNetworx for DeviceNet in the DeviceNet parameter group for these parameters:
Comm Flt Action
Idle Flt Action
The default value is the most conservative action; fault the drive when either event occurs. I usually set my drives to Stop when an Idle or Comms Fault occurs. That way I don't have to manually or programmatically reset the fault.
An alternative is to have the controller automatically reset the fault over the DeviceNet link. Bit 02 of the command word is the Reset Faults bit.