Geometry modification changes model behavior

I have a relatively complex model that is 14mm by 10 cm by 10 cm. It's a simulation of an evaporator for a heat pipe and features some inflow and outflow ports for the working fluid, water. One of the important phenomena is the temperature distribution once the water enters the device. The simulation runs convection and conduction and Darcy's law.

I realized I needed to make some small changes to the geometry of an internal feature. I expected a small but noticeable change to the temperature distribution mentioned above. I made the change by deleting the internal feature, rebuilding it, and then re-extruding it. After ensuring all boundary conditions and subdomain settings were correct, I re ran the simulation. The temperature distribution looked roughly the same, with an important difference: the liquid inflow was not having any effect on the temperature distribution (ie I was getting only conduction, and not convective effects). After checking this, I did not see anything that would explain this behavior.

I tried again, rebuilding the internal geometry to its original configuration and taking the same steps, to the same result. I noticed that the 'u_chdl, v_chdl, and w_chdl' weren't set in the subdomain settings for the water. Modifying this produced the desired change on the original geometry, but not the new, modified geometry. Multiple trys have not reproduced the result.

Any advice?