First; I assume you have backups of this data (on tape or so), just in case. After this assumption, I'd suggest indeed to do a normal shutdown of the server. Then power down the MD1000 (both power supplies). Give the MD 30-60 seconds to spin down the drives and fans. Power up the MD1000 again, give it 2-3 minutes to spin up the drives (ignore any fault lights for now). Then power up the server and see if you can see the drives (either in the PERC bios or in the OS/OpenManage). If not, shut down again and move the SAS cable to the other controller on the MD1000 to see if it's maybe just the EMM (be sure to connect to the in-port, not the out-port).
We have a dell Poweredge 1950 running Windows Server 2003 SP2.  The server has a Perc 5/e card that is connected to an MD1000.  The MD1000 has 6 700GB SATA drives in a raid 5 and 6 2TB SATA drives in a raid 5.  It has been working fine for years.  We use the drives for backups.  This morning I noticed all of our backups had failed last night.  When I went to look I noticed that the drive letters were missing from windows.  I checked the windows event log and noticed that there was an error . SCSI sense data Sense key:  3 Sense code: 11 Sense qualifier:  0:  Physical Disk 0:0:10 Controller 1, Connector 0 About 2 hours later there was a percsas event: The driver has detected a device with old or out-of-date firmware.  The device will not be used. Then there are some errros about the perc 5/e having disappeared from the system without being removed properly.  Long story short is that I can't access the data.  In dell open manager it shows that one of the raid 5 arrays are degraded but all the physical drives are still there and appear healthy.  I can also see the perc 5/e card and that the md1000 is connected to it. I haven't tried anything because of fear of losing data.  Should I reboot the server and see if the drives appear again or should I try something else first to ensure that my data is safe?  This has been running as is for 4 years and we haven't updated anything that would have caused a firmware error.
Issue with Perc 5/e and MD1000 Enclosure