Nick,
After you power everything down and get your unit back in sync, consider doing what I do, and use the ETEKCITY Zap Remote Control Switch on your complete layout. It work great and this eliminates having to use the e-stop. The unit comes with 5 different plug in control switches, and 2 HHRC units. I keep the 2 HHRC's around the layout for easy access during any kind emergency shut down. Give it a try the method works nicely.
The ETEKCITY ZAP remote controls are available right off the Net, delivered right to your door.
PCRR/Dave