You have the option to migrate EFS certificates when using USMT. If Scanstate comes upon a file that is encrypted, the migration will fail. If you have EFS enabled in your organizations, include the /efs:CopyRaw tag in your ScanState command line. No additional switches are needed with LoadState.
What about your other digital certificates. The reference below shows to other methods to migrate your EFS certificates. These can be modified to help migrate your other digital certs.