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Yubikey nanos are the way out of that specific problem

I imagine Yubikey doesn't support all the stupid custom-app-2fa that companies push out.

I really wish they'd just stick to classic TOTP.

Is there a way of getting them to store a dozen or so totp secrets? And if so, how do you select which one you want to use?

For that use case get an onlykey rather than a yubikey.