For all those of you who have been trying to clear Putty’s cache of host fingerprints (Windows) for development or testing, here is the answer:
1. Open the registry (regedit)
2. Go to HKEY_CURRENT_USER\Software\SimonTatham\PuTTY\SshHostKeys
There you should see Putty’s cache of host keys.
The ‘name’ column tells you which key is for which server.
For example, it will have the format of @ : [rsa2@22:172.16.117.159]
3. Delete the rows that you need and presto!
That’s all there is to it.
Reference : Clear Putty Cache