Sage has an interesting knowledgebase article that describes how to delete a warehouse from MAS90 and MAS200 Inventory Management. As you likely have discovered if someone creates a warehouse and makes an entry into that warehouse then you’ll be prohibited (“You may not delete an active warehouse”) from deleting the warehouse.
Sage’s article advises running the Stock Status Report for the specific warehouse and zeroing any items shown on the report. For details take a peek at the official Sage KB.