I have been using VestaCP for quite a while now.
I had the same issue before, but it seems to have been fixed with 0.9.8-16. However, with -17 it seems like its back.
My DNS Server entries loses its entries after a certain time. I am using it for dynamic DNS, my nodes connect via SSH to the main server and use v-change-dns-record to update the entry. Thats usually working fine, but it seems that after some time, the DNS entries kill themselves. Both, the db in /home/$USER/conf/dns/ and the config file in /usr/local/vesta/data/users/$USER/dns/ are just empty. Thats only happening to the DNS domain that hosts the dynamic DNS, the other DNS domains keep untouched.
Any help would be greatly appreciated and I'll gladly provide any log that's necessary.