The 9185 is a Time Aware chassis. The 9239's are Delta Sigma modules. If you were using LabVIEW and DAQmx, the two 9239's would be automatically synchronized to the 9185's clock.
Below is the relevant snippet from the link: Signal-based Synchronization of Analog Input C Series Modules with NI-DAQmx in LabVIEW - NI
Two Delta Sigma Modules - When two Delta Sigma Modules are placed in the same hardware timed AI task, the DAQmx driver shares the fastest master timebase between all the modules, resets their ADCs based on the same synchronization pulse, shares a start trigger, and adjusts the reset time. The master timebase is the internal 12.8 MHz or 13.1 MHz clock that Delta Sigma Modules use to acquire measurements. The default behavior for an cDAQ-9185 or cDAQ-9189 (time-aware chassis) is that the master timebase originates from the chassis instead of the module with the fastest master timebase.
In short, FlexLogger should automatically synchronize these modules as well. Have you verified the phase delay isn't somewhere else in the hardware chain? You could do this with an oscilloscope, but the fastest way to verify might be to double lug a wire between the measurement on one card to an unused channel on the second card. If you are seeing a phase delay on what is essentially the same signal, then you have potentially confirmed some phase delay between the two modules.
