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Would you mind clarifying what it would mean to disable a query?
Today, you are able to fundamentally remove 2 components for a query:
And it won't be considered for the refresh or evaluations assuming that such query is not referenced by other queries that don't meet the two (2) requirements above of not having staging and not a data destination.
We also do allow you to "save" at any given time. We do run some validations to prevent you from saving something that could potentially have some bad repercussions. However, if you've encountered one validation that is simply preventing you from saving and blocking you, please let us know and we could assess the impact and address such situation.