FND_NODES gets populated by AutoConfig, not by Preclone ... to my knowledge.
Here's the order:
Stop the complete middle-ware
AuroConfig ALL middle-ware nodes
Create appsutil.zip on 1 middle-ware node
Copy that file to ALL DB node(s)
Extract appsutil.zip on all nodes
AUtoConfig on ALL DB nodes
run Pre-clone on each tier
Take a backup of the environment, which you can use for cloning purposes
Yes fnd_nodes tables are updated with autoconfig.
Make sure that you execute autoconfig first on database nodes then on application nodes.
X A H E E R
"Make sure that you execute autoconfig first on database nodes then on application nodes."
You may be right, if FND_NODES is empty
But, to have appsutil.zip correct, first you need Apps and then DB