Hi I have an issue with a zone on my custom map and I need to remove it can this be done via any rcon console or ingame command.
Thanks in advance.

I assume you don't mean a zone made with Zone Manager?
If you do, in that case you can just /zone_remove <zoneID> in game.
To get a list of your zones and find the zoneID, use /zone_list in game.

I wish I had created in zonemanager but It was created on the map with rustedit. I tried creating a parent zone with zone manager but the map flags overide its settings.