I don't think it is actually used somewhere, but I wrote an article about using Yubikeys with Fedora a long time ago when the Infra team was busy implementing Yubikey support. Iirc I wrote about using the second slot somewhere in there. It might help you: https://fedoraproject.org/wiki/Using_Yubikeys_with_Fedora

Maxim Burgerhout
maxim@wzzrd.com
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On Thu, Oct 13, 2011 at 11:45, Thomas Spura <tomspur@fedoraproject.org> wrote:
On Tue, 11 Oct 2011 23:02:36 -0700
Toshio Kuratomi wrote:

> On Tue, Oct 11, 2011 at 11:11:39PM -0400, Paul Wouters wrote:
> > On Tue, 11 Oct 2011, Nathanael D. Noblet wrote:
> >
> > > As far as I know if you burn the key you will lose the ability to
> > > use the yubikey's servers and I'm guessing coincidentally the
> > > lastpass as well. I have seen that you are allowed to upload a
> > > new key to their servers to restore its useability. So that may
> > > be one avenue to look into.
> >
> > If these keys are still the AES symmetric keys, do not upload them
> > to any third party - those type of keys cannot and should not be
> > used with different entities. I thought the newer yubi keys had
> > more then one slot though, so perhaps one slot can be used for FAS,
> > and the other for the yubisoft servers.
> >
> I currently have my yubikey set up to do this (slot 1 is Fedora, slot
> 2 is for yubikey servers).

Could you describe how you did that?
All I could find is this instruction set [1].

Maybe that could be added there.

Thanks.
 Tom

[1] https://fedoraproject.org/wiki/Infrastructure/Yubikey