There's no syntax that can magically change the source from non-nullable to nullable in a Modify stage. You can, however, specify that the target is nullable.
Can you take a look at the job log to see whether any particular process takes a very long time? Perhaps enable some of the reporting environment variables (especially APT_PLAYER_TIMING)?
You have to find the previous run FOR THAT INVOCATION. If there have been many runs with different invocations that particular previous run may already have been purged.