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Any idea why all these files got lost?Absolutely none. HP would be your best source of information about that program, pun intended.
Now, given that I know absolutely nothing about how that program works internally, I would suspect that at some point it resets the SCSI controller which then takes abnormally long to complete. When the program resumes, the SCSI devices aren't available because the SCSI controller is still resetting.
Do you have anything showing up in /sys/bus/scsi/devices?
Which driver are you using? HP support expects you to install their special "cciss" block driver. You might want to do a "lspci -v" to find out what driver you are using.
Other than that, HP provides support packs for Linux including firmware updates. You might want to check you have the latest firmware updates installed and also verify you use the latest tools. The current acu utility is version 9.4. HP has provides its own YUM repository that makes updating software easier. I'm not sure if they provide any kernel drivers for Oracle UEK.
My guess is that you can probably ignore the issue. You can also boot into the ROM utility of the adapter to configure your storage system when the system starts, which is probably the best way.