I would double check the patch input impedance, to make sure the good match is with 100 Ohm port (not the default 50 Ohm). Also, I would double check the port impedance for the model with line.
Resonance: There is certainly a little influence when extending the feed line, if the initial model had some residual coupling between EM port and path. But it shouldn't move you resonance too much. How much shift do you see?
Can you show your Momentum mesh? Coarse mesh that changes a lot when changing geometry details might explain your issue.