Methods for compensating for the warp exhibited by three-dimensional glass covers as a result of ion exchange strengthening are provided. The methods use a computer-implemented model to predict/estimate changes to a target three-dimensional shape for the 3D glass cover as a result of ion exchange strengthening. The model includes the effects of ion exchange through the edge of the 3D glass cover. In an embodiment, the inverse of the predicted/estimated changes is used to produce a compensated (corrected) mold which produces as-molded parts which when subjected to ion exchange strengthening have shapes closer to the target shape than they would have had if the mold had not been compensated (corrected).