With a new version of MineCraft coming out I'm worried that all the chests will become unregistered, again. Is there any way to avoid this? Do we just leave the server on an older version of MineCraft until the plugins are updated for the newest version?

The chests unlocked on the last update because we switched from canarys-mod to bukkit
it never happend during an update before.
only once due plugin failure.

So no worries.

WHEW. I did not want to risk my chests being raided again.