Hi @zerkms,
As far as I know, the directories /etc/letsencrypt/keys/ and /etc/letsencrypt/csr/ are there just for backup purposes, anyway, @schoen and/or @bmw could have a better answer.
Also, there is an open issue to deprecate these directories https://github.com/certbot/certbot/issues/4634
Cheers,
sahsanu