hi Tarzan,
Would you be able to sent NACK instead of ACK before the STOP command is issued? This is raw 14 in your excel file.
I will run similar experiment myself to make sure we get consistent results between the two setups.
With respect to your Q1:
The AD7995 doesn't need an external clock for internal bit trials. It uses an internally generated clock for that purpose. If you stop supplying clock during a middle of conversion of, say channel Vin2, the part will finish this conversion anyway. Please be however noted that the AD7995 was not designed to operate under these conditions hence I would recommend to reconfigure the part as soon as the communication is established. This would help you to ensure that the part is converting on the desired channel.
Best Regards,
Jakub.