IM / MDIS is currently not able to delete records. The right place for deletion is the Data Manager. A good approach could be a "deletion flag" maintained in remote systems and MDM. You could use IM / MDIS to import this deletion information (in other words mark the MDM records for deletion). Then you can open DM, search for the records that are marked for deletion, select all and delete them. you could even think about using a MDM Workflow for some fine tuning of the process (maybe check out the records thus they cannot be used by others, create a eMail notification for the user being responsible for deletion, and so on).
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