Luis,
You can use the Optomux commands to reset the FP-1001 programmatically. The supported Optomux commands are described in the FP-1000/1001 Programmer Reference Manaul. There is a FieldPoint LabVIEW Optomux library, although it is only installed by default if you have LabVIEW RT installed. Otherwise, you will need to re-install NI FieldPoint and choose Custom installation. Select the LabVIEW FieldPoint Optomux support during the custom installation.
The correct command to reset the module is the !Z Reset.
Regards,
Aaron