Generally speaking the answer is “yes.” You can approximate the connector or any other discontinuity (bend, trace, via etc.) with IConnect model and then obtain another open or short reference to calculate the S-parameter data. To illustrate this, consider the time domain data shown in figure 1. The DUT data, red waveform, indicates an inductive discontinuity right after the green reference (Old Reference). The goal is to de-embed this discontinuity and shift the reference plane to the new location (New Reference). Simply modeling the discontinuity and then acquiring the open-ended reflection for the model could obtain the new reference plane here. This will create a new reference (blue line) as shown in the figure 1.
Figure 1. Time domain data that was used to calculate S-parameters.
Finally, the new open reference and the DUT data is used to calculate S-parameters for the new reference plane. The resulting S11 data for the old and the new references is shown in figure 2.
Figure 2. Calculated S11 data for the old and the new references