First you need to have LSI's megacli installed. See how here:
# Get info on RAID arrays
sudo megacli -ldinfo -lALL -a0
If you cannot find an array where state is not (Partially) Degraded don't do any of the steps below!
# Find drive that needs to be replaced or rebuilt
sudo megacli -pdlist -a0 |egrep "Enclosure Device|Slot|Firmware state"
# The drive coordinates look like [enclosure:drv_id]
# Make the state to Unconfigured(BAD)
sudo megacli -pdmarkmissing -physdrv[0:6] -a0
# Make device state good
sudo megacli -pdmakegood -physdrv[0:6] -a0
# Verify that the array started rebuilding
sudo megacli -pdlist -a0 |egrep "Enclosure Device|Slot|Firmware state" | grep
Rebuild
# You could also use megasasctl
# sudo megasasctl
Links with useful info: