Doing a fresh install would skip some parts of what the install script does.
I've been attitude adjusted to Windows programs writing to registry and therefore making simple copying and delete less useful.
On the other hand java programs were supposed to be platform independent.
You can see some opinions on where Clarity is in this relation in
Copying the application binaries from 32 bit to 64 bit
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If you are not happy with copying, you could use nikuadmin backup and restore the backup to you new server.
Martti K.