Update: It turns out there is a very good reason to move to 2048-bit RSA keys (if you haven’t done so already — again, that’s the default behavior for ssh-keygen and it has been for quite a while now): according to this paper, 1024-bit keys make your system more vulnerable to the recently (Oct-2016) discovered “Logjam” attack.
The details are too technical even for me, without a lengthy deep-dive, YMMV.
So, I’ve done a (very little) bit of experimenting, as this post surprised me, and I thought I may help clarifying a couple of points:
ssh-keygen
with no arguments, by default will generate a 2048-bit RSA key (by default in ~/.ssh/id-rsa but you have the option to change that).
Also, upgrading to Sierra will not lock you out of your servers, if you are using regular RSA keys (I must assume it does if you use DSA keys, but I wouldn’t know, because, in 10+ years of managing servers and generally messing around with Linux, I never used them…): my RSA keys (both public and private) were still there in my .ssh folder after upgrading (I just checked out, fearing the worst!) — so maybe your title, while compelling, may be a bit too alarmist for most folks out there.
Finally, you always ssh into your servers using your private key — I am guessing that the ssh client is smart enough to figure it out if you give the public key to look for a “sibling” file without the .pub extension.
And, BTW, if your private key is the default ~/.ssh/id_rsa you don’t even need to specify that, the ssh client will find it (you can also specify a set of keys to try out by changing some configurations, but that’s an entire blog post by itself, probably).
Hope this helps!