Certificate issue

Good day,

I’m encountering a strange issue regarding one of the virtual domains SSL certificate.
A couple of weeks ago I’ve received hundreds of emails that said that there were too many requests to Let’s encrypt to renew the certificate for domain.tld(the domain was not expired yet). In the Letsencrypt page the certificate had the recent date as the Last successful renewal but accessing the website there were an error present as bad domain certificate.
Now the issue is that the certificate is expired, the Letsencrypt generates a new certificate, but on Setup SSL certificate → current certificate, the information is for the old certificate(the one that is expired) as if the new certificare is not taken into account.
I’ve restarted the Apache several times with no change(no errors were present), disabled and enabled the website SSL with no change. Renewed the letsencrypt certificate several times with no change.
Basically the old certificate is still taken into account(/home/domain/ssl.cert/key/ca) and not the /etc/letsencrypt/live/domain/cert.pem…).
If I’m deleting all the ssl.* files in /home/domain I’m unable to activate/deactivate the website SSL for this virtual domain. Also the renewing of the certificare did not created new certificates in that path.
Any ideas on how to solve this issue?

OS type and version Debian 10
Virtualmin version 7.9.0