I tried your suggestions, and after adjusting the imaginary weight in the materials explorer, the # of coefficients, fit tolerance, etc. were the same. That improved the JSC in the pyramids solar cell (w/ the deactivated pyramids) by around 2 mA/cm^2, but it's still at 16.7 mA/cm^2 vs. 19.0 mA/cm^2 for the planar silicon cell. Do you have any other tips? I would not have thought to change the imaginary weight if you hadn't suggested I look at material fit, so other troubleshooting tips would be much appreciated!