What is the best way to query deleted records with SQL Server 2016 temporal tables?

Temporal tables are intended to give you a point-in-time view of your data, not a state view - it doesn't actually understand state. Nothing is exposed to users to determine how a row arrived in the temporal history table.

If you did not temporarily pause/stop system versioning on your temporal table then you just need to find the delta between the history table and the active table. All remaining rows in the history table that don't have a corresponding row in the active table are deleted rows.

For example, if you have tblCustCalls and it's enabled for temporal with a tblCustCallsHistory, something like SELECT * FROM tblCustCallsHistory WHERE ID NOT IN (SELECT ID FROM tblCustCalls). In this example, ID is the primary key. You can optimize the TSQL if the tables are very large but the base concept doesn't change.