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Ssh keys problem

I'm new to ssh, so bear with me if I'm going about this the wrong way.

Two days ago I thought I had this working correctly, apart from the fact that 
it regularly complained that it couldn't find one of my gpg keys.  Since I am 
concerned only to use it for ssh file transfer, solving that problem is not 
urgent.  Yesterday I found that it was asking for the password for every 
transfer, and I'm sure it wasn't the day before.  I've done one transfer this 
morning, and this is what happened:

Warning - the authenticity of host 'borg ('... can't be established
RSA key fingerprint is ......
Are you sure you want to continue?

Permanently added 'borg' (RSA) to the list of known hosts.

It's perfectly possible that, when I made a boo-boo on transfering some files 
from my home directory a couple of days ago, I could have overwritten 
something.  In fact, I think that's the most likely reason.  Question is, 
though, how do I go about troubleshooting this?  Should I delete the .ssh 
directory on the remote box so that I have to start afresh there?


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