How to subtract records from a table based on their existence in another
It seems the answer was hiding in plain sight:

DELETE a.*
FROM Import AS i INNER JOIN Assignment AS a 
ON a.Empl = i.Empl AND a.Year = i.Year AND a.Week = i.Week


or

DELETE a.*
FROM Import AS i INNER JOIN Assignment AS a 
ON a.Empl = i.Empl AND a.Year = i.Year AND a.Week = i.Week AND a.Proj &lt;&gt; i.Proj


depending on which is most appropriate.

I don't know how I failed to see it first time around!