James,
In general, it isn't possible to reestablish the connection for some
devices. A lot of it is the drivers of devices themselves and how JMRI
binds things together. A few things like network connections have the
idea from the start that the physical layer may have to
restart/reconnect. Most other things never had that as a design
feature.
Also having JMRI sit there playing are you there isn't a great use of
computing power. All sorts of internal things are cleaned up only on
the exit and later restart of JMRI. That's just the cleaner and safer
way.
-Ken Cameron, Member JMRI Dev Team
www.jmri.org
www.fingerlakeslivesteamers.org
www.cnymod.com
Ken Cameron