remove the server manually from server table in the ispconfig database of the master. note down the server_id of that server before you delete it. Then delete all records in the sys_datalog table for this server_id.
I have a similar situation where I have deleted VM ispconfig's incorrectly. If I do SELECT DISTINCT `server_id` in sys_datalog I get 0, 1, 3, 4, and 7 returned. If I look in the server table I can see server_id 1 for ns1 and server_id 7 for ns3 in this case. Is it safe to delete all entries in the sys_datalog file with 0, 3, and 4 ?