Well, it did come back up and started a parity check. It then hung during the parity check. I've now removed the harddrive and am running unprotected.
The drive never has had any issues with it up till now, it is about 4 months old.
I took the drive out, rebooted, deleted the file I had the original trouble with, shutdown, put drive back in, rebooted. It is now rebuilding the server, and will be done in 1682 minutes! Wow that is a long time!
Hopefully all will work out in the end.