any time you are bringing data into the DW using a Delta you will potentially have records that are not in the Delta. This may be because they are outside the scope of the Delta or because they have been physically removed from the source data. If this is important to you then you will need to run a cleanup script to identify records you expected to see in the delta but were not there and have to assume that they have been deleted and mark them appropriately.

This still leaves you an issue with how to identify records which you are not expecting to be in the Delta but have been removed from source.