let's encrypt mismatch cert and key

I got into a situiation where I could not renew the LE certs without doing again register:

$ leap cert renew mydomain.com
 = bailing out                                        
   - missing file files/ca/lets-encrypt-account.key
   - Please run `leap cert register` first. This only needs to be done once.
$ leap cert register
 = registering letsencrypt.org authorization key using contact `root@mydomain.com`
   - success!
 = saving authorization key for letsencrypt.org
   - created files/ca/lets-encrypt-account.key
   - created files/ca/lets-encrypt-account.json
   - warning: keep key file private!
$ leap cert renew mydomain.com
 = checking authorization
 = uploading challenge to server mydomain.com
   - [node] Uploading /srv/acme/7lvctND1_VxaBY3jPaXTyvcv_vgFqDQRG3ajtX2QvDM 0.0%
   - [node] Uploading /srv/acme/7lvctND1_VxaBY3jPaXTyvcv_vgFqDQRG3ajtX2QvDM 100.0%
 = waiting for letsencrypt.org to verify challenge
 = authorized!
 = fetching new certificate from letsencrypt.org
 = success
 = updated files/cert/mydomain.com.crt
 = You should now run `leap deploy` to deploy the new certificate.

After doing a deploy the key and the cert in the node are not matching and apache doesn't work. So I can not do a new renew or anything there.

(from redmine: created on 2016-12-30)