You need to change the keys. On your instance use ssh-keygen to do this e.g.
ssh-keyget -t rsa -b 2048
Enter file in which to save the key (/root/.ssh/id_rsa):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /root/.ssh/id_rsa.
Your public key has been saved in /root/.ssh/id_rsa.pub.
The key fingerprint is:
35:dc:34:c2:98:89:8b:4a:e2:f7:71:ad:09:02:83:57 root@somehost.tld
Now you have a public key (/root/.ssh/id_rsa.pub) that needs to be added to the /root/.ssh/authorized_keys
file
cd $HOME/.ssh
cp authorized_keys authorized_keys.safe
cat id_rsa.pub >> authorized_keys
You'll have to remove the old key from the authorized_keys file later.
Don't log out.
Copy the new private key (/root/.ssh/id_rsa) to your windows machine and use puttygen to import and save it like you did previously.
Check that you can log in using your new keys. If you can then remove the old key from your instance.
cat id_rsa.pub > authorized_keys
Don't log out.
Now check again that you can log in using your new keys
You really shouldn't use the root account in this manner. You should create separate user accounts for everyone that needs access to your system. You should then use sudo to grant them access to the commands they need to do the job. Sudo is part of the base install for most (all ?) Linux distros.