No you can't just rename a -delta.vmdk to a -flat.vmdk, because the delta is a bitmap of the changes that have occured to the base -flat.vmdk on it's own it is meaningless.
To achieve what you want, power off the VM, use vmkfstools -i to make copies of the base VMDKs and all the delta's (always point at the .vmdk header files not the -flat.vmdk or -delta.vmdk when working with vmdk files). Then copy the .vmx and .vmsd files over, edit the .vmx file to reflect the new paths where you cloned the vmdk files too, likewise with the .vmsd, and change the name in the .vmx. Then register the VM with a host, power it on, and when asked create a new UUID. Voila, you have a clone with the snapshot tree intact, it's a manual process, but not too difficult.
