system/messages/messages_*.properties was deleted in upgrading

[Rod Widdowson]

> Nothing in system/... is ever preserved during upgrades.

Now I'm back at my desk in [1] it says 

> "system" : Contains read-only internal system configuration that should not be modified.
> The contents of this directory tree will be deleted and re-created by an install or upgrade.

You need to put youe messages into the "messages" directory.  The behavior of this changed in V3.3 to be more in the expected line
[1] again says:

> As of V3.3, this contains only new or overriden message properties or post-install translations, 
> with all of the default messages and translations moved to the system tree.

Hope this helps

Rod

[1] https://wiki.shibboleth.net/confluence/display/IDP30/Configuration#Configuration-InstallationLayout