Open a command prompt and go to the Plesk admin bin directory. Most likely: C:\Parallels\Plesk\admin\bin or C:\SWSoft\Plesk\admin\bin. E.g:
cd C:\Parallels\Plesk\admin\bin

 
Run the following command:
dbclient.exe --direct-sql "--sql=select id,name,status from dns_zone"

This will show you a list of all the domains in the BIND service on your server (i.e. domains added to the VPS). Any entry with a 2 beside it usually means an error. In this case there would be two entries for your_domain_name.com, one with a 2 beside it, as it was an incorrect duplicate entry.


What you need to do then is note down the ID number to the left of the entry for the duplicated domain name (the one with the 2 instead of 0 at the end) and then run the following commands:

dbclient.exe --direct-sql "--sql=delete from dns_recs where dns_zone_id=XX"
dbclient.exe --direct-sql "--sql=delete from dns_zone where id=XX"
where XX is the ID number. In this case it is 10.


Then finally run one last command to update BIND on the server:

DNSMng.exe update *