Hi @Magnus ,
Thankyou for using Microsoft Q& A platform and thanks for posting your query.
As I understand your query, you are trying to perform Upsert in SQL table which is having Employee ID as identity column . However, it fails when you are removing EmployeeID column from mapping so that it automatically inserts the EmployeeId value. Please correct me if my understanding is incorrect.
I tried to reproduce your scenario and witnessed same issue. Insert is working fine after removing the identity column from mapping while upsert is failing.
I have raised the issue with internal team , will keep you posted once I hear back from them . Thankyou for your patience!
Meanwhile, temporary workaround is to create custom Stored procedure to perform the Upsert using Merge statement.
Please check the following article for the help : Invoke a stored procedure from a SQL sink