In reply to tpan:
You can run sequences in parallel on a sequencer. But even in this case seq_items are generated in a series. It starts randomly if you do not set the priority. And I believe it is uesless to reconfigure your DUT accidently during operational running.
The options you have is structure your sequences in the right way. Or if you are waiting for a certain situation before reconfiguring you can do this using lock or grab. This will interrupt your operational mode and you can continue after reconfiguration.
Again ther is no need to use the sub-phases.