Why does letsencrypt create new certificates in a new directory?

Question

Digital certificates

When creating a new certificate, letsencrypt creates a new domain-0001 folder with new certificates, and the old domain folder contains valid certificates and I don’t understand how to update them.
As I understand it, everything is due to the fact that the new certificate does not contain subdomains that I no longer need. The
old certificate was issued to the following domains

domain.ru
www.domain.ru
static.domain.ru
tmp.domain.ru

I'm trying to get a new certificate for the following domains

domain.ru
www.domain.ru
img.domain.ru

As a result, letsencrypt creates a new directory domain.ru-0001, and I just need to simply overwrite the previous one.
I'm trying to overwrite it with this command

certbot certonly --force-renewal -d domain.ru -d www.domain.ru -d img.domain.ru

I tried to delete all unnecessary information related to domain.ru-0001 Deleted the
folder /etc/letsencrypt/live/domain.ru-0001 Deleted the
config /etc/letsencrypt/renewal/domain.ru-0001.conf
Another attempt and everything is repeated, a new one is created folder?
What can be done?
Move certificates from the domain.ru-0001 folder to the domain.ru folder?

Answer 1

In general, with my problem, the solution seems to be to specify the name of the certificate in the request.
Then it says that a new domain will be added, and the old unspecified ones will be deleted.
So this should work!
Now only the limit has been exhausted, and we must wait, writes

An unexpected error occurred:
There were too many requests of a given type :: Error creating new cert :: too many certificates already issued for exact set of domains: ....домены... see https://letsencrypt.org/docs/rate-limits/

Answer 2

You, apparently, for some reason removed the symlink to the directory with the current certificate, which certbot automatically modifies with each update. In itself, the presence of all these directories with numbers is normal.
Use /etc/letsencrypt/live/domainname/fullchain.pemand /etc/letsencrypt/live/domainname/privkey.pem, in general - they will always look at the current version.