Are you hard deleting the record or soft deleting it?
Which SOAP API you are using and what parameters you are passing?
As rightly pointed by Sakshi, we have two types of delete process in MDM layer.
Soft deleting a Record -- When you are using 'delete' API from Soap UI
Hard deleting a Record -- When you are using 'ExecuteBatchDelete' API
If you are using Delete API, the data will still be present in BO, only with hub state ind = -1