Logged a call and the solution was as follows:
NB: Remember to backup your DB in full before doing this as it's at your own risk!!
- Lookup the component_name_id for the inventory node you need in inv_table_map table. The component_name column should map to what you see in DSM explorer
- Use this component_name_id to rmeove the link for that inventory form inv_root_map
Essenitally that removes it from the Inventory tree in DSM explorer but still leaves 2 tables for each custom inventory behind and orphaned in the DB. Finally you can rmeove data or drop these tbales
- ca_itrm.inv_<component_name>_tree
- ca_itrm.inv_<component_name>_item
Where component_name is the name of the custom inventory located in 1 above.