A computer system includes a Flash or other nonvolatile memory. A program(s) to coordinate data transfers is loaded into a volatile system memory to transfer data from an external device to the Flash memory. The data transferred from the external device to the Flash memory can be transferred to a previously unused portion of the Flash memory, or alternatively can overwrite a previously used portion of the Flash memory. According to one aspect of the invention, the data is transferred from the external device to the volatile system memory and then from the volatile system memory to the Flash memory, allowing additional verification steps to help insure that the data is transferred intact. According to another aspect of the invention, data is copied from the external device to the Flash memory on a portion by portion basis, leaving a set of critical portions to be transferred last.