In the original 653x User Manual there is a note describing how to reverse the pin assignments of ACK1 (PFI6) and REQ1 (PFI2) so that two 653x devices can handshake with each other. How can this be done with DAQmx?
This behavior can easily be performed in NI-DAQmx. You should first download the NI 6533/6534 for NI-DAQmx Help. Information about the different properties that can be used can be found in that help file under Sample Timing Types»Transferring Data Between Two Devices–Handshaking»Handshaking Attributes/Properties. Of special interest would be the Handshake Event Output Terminal property and the Handshake Interlocked Source property. By setting these properties to the desired PFI lines you can effectively switch the lines.