this is probably a dumb question, but why not just store a secret seed that is used with an on device prng to generate as many secrets as you need where a sequence id gets shared with the counterparty?
The main feature of resident (aka discoverable) keys is that the RP doesn't need to know anything about which key is about to be used, so it can just say "send me an auth for example.com", and the browser and key handle the rest.
However, with non-discoverable keys, the RP has to provide a reference to the key, which could actually have encrypted private key matter in it.