In the dio_hw.pdf hardware note,

in Figure 3.1 the input comparator is shown to be driving the DIFF_IN signals, and the output buffer is shown to be driven by the DIFF_OUT differential signals. This is probably the most sensible assignment from the point of view of the function the device is going to play: to output a signal into the LEMO connector or to receive an input signal from the LEMO connector.

In the EDA-02408-V2-0 schematics, instead,

the input comparator is driving the OUTXY_P/OUT_XY_N differential signals, and the output buffer is shown to be driven by the INXY_P/IN_XY_N. This latter signal assignment is, further, inconsistent with the output enable negation signals (OEXY_N) that enable the output buffer.