It is ok to use Let’s Encrypt certificates, is there any reason you want to pay for a certificate?
Anyways, you could try to update the cert from command line, create a dir (for example /tmp/cert/) where you will copy the certificate, the key and the ca-bundle and the files must have this format (I’ll use example.com as the domain):
example.com.crt
example.com.key
example.com.ca
Then execute this command (replace fortune by your actual Hestia user):
v-update-web-domain-ssl fortune example.com /tmp/cert/ updatessl