How should I proceed to add a new cert based on that information?
Would just a certbot certonly and put only the sudomain dev.sekretyrozwojuosobistego.pl when requested would be enough, or it would delete the old certs?
Also, I wish I could keep the same nginx configuration, I mean to not create new file/folders, but to update the existing ones:
Unfortunately, certbot doesn't have a good (or any at all) interface for adding or removing hostnames from an already existing certificate. This is already known to the certbot team but hasn't gotten much attention unfortunately.
The best way to add or remove a hostname from an already existing certificate, is to use the same command as you've used to get the certificate in the first place and add (or remove) the extra hostnames you want to add. It's also always a good idea to use --cert-name so certbot knows exactly which certificate to update, so you don't end up with two separate certs.