UPDATED: NOVEMBER 17 2016
Deactivating a scheduled report would be more ideal than deleting it simply for convenience reasons. If you are looking to temporarily halt the distribution of a particular scheduled report, and you intend to reactivate it at a later date, then deactivating the scheduled report would prevent you from having to create this Scheduled Report again from scratch.
On the other hand, if you are not planning to send out this scheduled report again, then you could consider simply deleting it.
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