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You should probably tell GitHub

I thought I deleted this comment. Sorry. Turns out I had an old key still in my .ssh folder. Two current and valid keys and no others. My bad.

Each fingerprint listed on my audit page was exactly what I expected it to be.

Sure you aren't confusing the fingerprint with the actual key contents?

I'm missing a whole bunch of keys – I previously had about 4 keys registered, now it's just one.

Did you contact support@github? We definitely want to know about that.