Metthieu,
You can use the UniFlash command line interface for this purpose. The command line tool supports a few different target operations that you can invoke after program load.
Here is the description of the targetOp parameter:
"-targetOp" is use to interact with the target after program loads. Specified multiple target operation arguments will be executed in order.
The current supported operations are:
1) "reset" - resets the target
2) "restart" - issues a restart on the loaded program
3) "run" - run the target core asynchrononously (ie; does not wait for a halt)
Please test this out and let me know if these options work for what you need. It is also possible to extend the command line tool (via DSS) to add additional commands as well.
Thanks,
Ricky