A picklist value is automatically deleted from the bucket when it is removed from the picklist definition.
For example, if you have bucketed opportunities by a custom Stage picklist value called Pilot and then deactivate that picklist value, the Pilot bucket entry is automatically removed from any report bucket columns referencing that field.
This is considered expected behavior. When a picklist value is inactive it is removed from the picklist definition and cannot be bucketed.
When a picklist value is deactivated, it is removed from the picklist field's active value set. Because report bucket columns reference the active value list to populate bucket options, deactivated values are automatically excluded from the bucket editor. Reactivating the picklist value will restore its availability.
Edit a Picklist Bucket Field
Manage Inactive Picklist Values
IdeaExchange: Ability to bucket on pick lists values that are no longer active
000384189

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