At the moment, the encryption for each file depends on
(nonce, masterKey)
I think what you are proposing is that we derive a per file encryption key
random = 32 bytes (say) of random numbers
fileEncryptionKey = derivationFunction(random, masterKey)
File decrytpted with (nonce, fileEncryptionKey)
We then store
(nonce, random) in the file in the clear.
This would mean that we could decrypt files as normal using the masterKey. We could also give people fileEncryptionKey for a single file without compromising masterKey.
I think that would work, depending on exactly what was used for the derivationFunction. A hash function keyed on masterKey would probably be the right approach or maybe we could use scrypt which rclone uses already, however that is quite computationally expensive.