The data remains in Panoply even if it no longer exists in the source because Panoply was designed as an analytical data warehouse.
If you want Panoply to contain the same data as your source, you can select the "Truncate" option. During each ingestion, this deletes and re-populates all data from the tables in Panoply associated with that data source.
On the other hand, if you delete data in your source and want to keep those deleted records in your data warehouse, you can filter them out for reporting by running a query where
__updatetime is greater than the most recent successful job's creation time.