Employee A created a query in Advanced Reporting and saved it to be used by others.
Employee B created a report and used Employee A's saved query for his report and made some changes.
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The changes made by Employee B in the query when he added it on his report will only be applied on his report and will not affect the query of Employee A.
It is expected behavior that the changes to the query done through Report Designer will not update the saved query. Once a saved query is used in a report, no dependency will exist between the query and the report and they are treated as separate entities.
For example, if you add an existing Shared Calculated column in your report and made some changes, it will not affect the original shared calculated column.
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Advanced Reporting Query Behavior, Shared Calculated columns behavior, Saved query behavior , KBA , LOD-SF-ANA-ADV , Advanced Reporting (ODS) , How To