We had an issue with an USB DOM in the past. As G-R said, I would also recommend to save the configurations constant. We had no problems to switch the USB DOM and load the old configuration file.

But I think the auto-save configuration files which will be saved on every shutdown are stored on the hard disks, aren't they? So it should be no problem anyway if you forget to save the configuration files.

Have you ever planned to use SATA DOM's? Might be more reliable.