Open
X:\PortableApps\PuTTYPortable\Data\settings\putty.reg and modify all references to the private key file to match the client you're updating the installation on (reference is from “master”). Be careful not to run the registry file, but to load it in your editor, the registry values are managed by the PortableApps loader. Note that back slashes need to be escaped in registry files.
"PublicKeyFile"="\\Security\\SSH\\master_id_ecdsa.ppk"
"PublicKeyFile"="\\Security\\SSH\\client_id_ecdsa.ppk"