After some research I managed to find some good old command prompt tools inside
%plesk dir%\bin %plesk dir%\admin\bin
1. Command line returned following error. (At least it returned some error rather than just saying it was successful).
An error occured during domain removal: Unable to remove domains: Unable to remove hosting: Unable to delete logrotate config: logrot_mng failed: Execute websrvmng --update-log-rotation "--vhost-name=[name_of_domain]" failed: Site [name_of_domain] doesn't exist.
2. I have then changed directory to admin/bin and ran following command
websrvmng.exe --reconfigure-vhost --vhost-name=[name_of_domain]
3. Remove domain.
domain.exe -r [name_of_domain]
This fixed my problem and left our Plesk server nice and clean.
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