Accurate cone-beam computed tomography (CBCT) reconstruction requires knowing the true geometric parameters of the scanner, obtained from calibrating the system. Positioning the detector panel offset to the source-detector axis is a technique used by linac-mounted CBCTs in the context of radiation therapy in order to image the full width of the patient over the 360-degree scan. However, offsetting the detector panel increases the difficulty of calibration as the resulting projections will be truncated along their width. We present an extended version of an existing phantom-based geometric calibration method that we have adapted for use in offset detector systems. This calibration method extracts the required geometric parameters from measured projection images of a specific calibration phantom we designed for use in the method. The calibration has been implemented in tandem with a variant of the Feldkamp-Davis-Kress (FDK) reconstruction algorithm which we have modified to both integrate our calibration and reconstruct width-truncated projections. The calibration and modified FDK algorithm are validated by the successful reconstruction of a simulated Shepp-Logan phantom generated with misaligned detector geometry (detector panel shifting, and variable detector panel rotation along the 360-degree scan). The method also applies to other types of detector misalignment. A physical version of the phantom has been constructed to validate the method with real data in the future.