Primary Key Violation

I am running in to a primary key violation. My target DE has 2 primary keys (ID+System) where there can be duplicate IDs and my source DE has primary key as ID. while update a column in Target DE based on matching ID, it throws me a primary key violation error

I cannot change the format in both source and target DE and have to so something with the query.

SELECT
a.ID as ‘ID’,
a.System as ‘System’,
a.Updated as ‘Updated’,
a.LocalId as ‘LocalId’,
‘TRUE’ as ‘IsDeleted’

FROM
[Contact Source] a Inner JOIN DeletedInvalid_Staging b on a.ID=b.ID

Could you suggest an solution for this?