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The main operation where you may experience incorrect results could be related to your Concatenate(LinkTable) operations.Given that you're trying to create a LinkTable by joining multiple tables on different fields, if these fields have common data between them, it might create duplicate rows which may, in turn, affect your sum(salary) calculation. You could also face issues if the department_id or employee_id fields have any null values. The null values might break the link between the tables and result in inaccurate sums. A good way to debug this would be to check the tables and fields being loaded and their resulting output at each step of your script.
You can use the Table Viewer (Ctrl+T in the script editor) to inspect your data tables after each load step. Check for any anomalies such as null values or unexpected duplicates. Additionally, for the sum(salary) issue specifically, ensure you have the correct associations between your 'Employees_Final' table, your 'LinkTable', and your 'MasterCalendar'. The association of tables in Qlik is based on common field names, and it's crucial for accurate calculations.