To ensure the cluster remains in a working state after a reboot of a nodes, we have a script to do a graceful shutdown.   

sudo bash /opt/ekco/shutdown.sh  

We have the following recommendations to shutdown.

• Use a cron job that executes the script 5 minutes before a scheduled maintenance. 
• We recommend waiting 30 mins between reboots. Linux OS takes at least 10 mins to reboot. 
• For unplanned reboot, have a manual process in place that includes running the script.
• Take regular backups of the VM.

If there's a lot of leftover failed or completed pods after a reboot use these commands to clean them up

kubectl delete pods -A --field-selector=status.phase=Failed
kubectl delete pods -A --field-selector=status.phase=Succeeded

If you have problems using redgate clone after a reboot, have a look at this troubleshooting guide.