Assuming that this mechanism runs at ambient conditions (RT, 50%rh) and each component has same tool texture, I think the softer material should wear most. Suppliers dont always provide hardness data, but this value might be related to tensile modulus which generally is. A dry, as moulded, unfilled PA66 will be stiffer than FR PC (3300MPa vs 2800MPa). However, moisture conditioning of the PA can reduce this by almost half. The short answer to your question, I dont know.
PA66 dimension changes due to conditioning might be important too.
If the part runs above RT, ensure that tool temperatures are between 90 & this temp. Warpage of the rod might ensue, causing more problems.
A better material combination could employ a PBT rod where moisture ingress would not be an issue.