which version are you using? 2008r2 or 2012? its a bit different depending on version but do not touch those mdm.tbl_9_99_en tables. You will want to insert records in to your staging tables with a 'delete' import type code.
This will hard delete the records out of your enviroment. To do this in T-SQL, you can insert the records into your staging table and then run the staging sweep stored proc (EXECUTE