The second hard driver (internal) was disappeared in my MacPro, after this update.

I found an error message, "the second hard disk was ejected", when my MacPro was resrarted after this security update 2013-003 .

The HD was diappreared in the system. I cannot find it in finder, disk utility, and terminal.

The other problem I just found is that some applications working with Java are not working.

Any suggestions or advice would be greatly appreciated.