For the first command, did you mean renew instead of run? Using run gave me the following error:
bitnami@ip-172-31-32-159:~$ sudo lego --tls --email="email@example.com" --domains="smc.bitnamiapp.com" --domains="www.smc.bitnamiapp.com" --path="/etc/lego" run --days=90
Incorrect Usage: flag provided but not defined: -days
lego run - Register an account, then create and install a certificate
lego run [command options] [arguments...]
--no-bundle Do not create a certificate bundle by adding the issuers certificate to the new certificate.
--must-staple Include the OCSP must staple TLS extension in the CSR and generated certificate. Only works if the CSR is generated by lego.
2019/05/07 05:29:03 flag provided but not defined: -days
Using renew gave me the same message saying "too many certificates".
As for your question, I really do not know. I followed several guides and jumped through 1000 hoops so far, so I may have done some things I wasn't supposed to. Does that configuration need to change?
I updated the bitnami.conf file and changed the values to point to server.crt and server.key and restarted the server. I still see an expired certificate on smc.bitnamiapp.com.