A couple of things come to mind.
“Renew” doesn’t use your cli.ini, it uses /etc/letsencrypt/renewal/your.domain.tld.conf. The settings used will be in there. Don’t mess around with the settings in there without knowing what you’re doing!
Also, I’ll bet that if you poke around in /etc/letsencrypt/live/ and /etc/letsencrypt/renewal/ there’ll be a bunch of domains => your.domain.tld, your.domain.tld_001, your.domain.tld_002, your.domain.tld_003, etc.
When you recreate the same domain instead of renewing, certbot leaves your existing certificate and conf files, and creates a new “001” version. It then creates new files every time, incrementing the suffix. It’s possible that this is confusing the renewal process.
You could try deleting every “your.domain.tld_00*” file and directory and leave only your original “your.domain.tld”, then try “certbot renew” again.
Ensure you don’t delete things willy nilly, as you’ll lose your account hash. You’ll see your account line in your original (and every other) /etc/letsencrypt/renewal/your.domain.tld.conf.
Keep the first certificate, cleans your system of the superfluous files, and try again. Keep in mind you’ll probably get renewal emails for every extra certificate you created. Ignore them. The deleted certs will expire and go away, and you can renew your original as needed.