Manually creating renewal config at /etc/letsencrypt/renewal/ helps
So does certbot certificates care /etc/letsencrypt/renewal/ info at the first place instead of /etc/letsencrypt/live?
How to make renewal config to be generated automatically with the certbot certonly call it self and based on all its attributes?
It sounds like you restored the /etc/letsencrypt/{live,archive} directories, but not the renewal/ directory.
All of the directories are required for Certbot to keep track of its certificates. renewal/ is where Certbot looks for information about certificates it is managing.
If you just drop files into live/ or archive/, Certbot will ignore them.
Certbot will always create entries in the renewal/ directory when you create a certificate. It is impossible for certificates to be written to /etc/letsencrypt/{live,archive} without a corresponding entry in renewal/.
Thanks guys for your feedbacks.
Looks like it is really a matter of /etc/letsencrypt/renewal being corrupted at my side.
Is there a chance to recreate its content (not manulally) having the rest of /etc/letsencrypt folders in place without generating new certs (it is a matter of hitting the limits now)?
Sure, someone with expertise and enough time could. But, it's far easier to just reissue a cert and let Certbot do its job
Given what you've described I don't see how rate limits apply. If you recently got 5 fresh certs for the same set of domain names then you have a recent one in /live/ which has enough life to allow you to wait another week to reissue. And, if the certs are older then they wouldn't be subject to rate limit yet.
Ah yes. To take a while before the next reissue was my second option.
I thought maybe there's something I can do just right now. Maybe something like hack as --dry-run with the same args and to capture renewal config from logs or something.