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Compress has the potential for deleting non leaf states while compress is executing, if users are editing simultaneously. When compress reads the state_lineages and states table into memory, there is potential where a new state’s parent state can be mistakenly deleted.
The compress operation reads the state_lineages and states table into memory as one of the first steps it performs when compressing the ArcSDE instance. If users are editing while the compress operation reads these tables into memory, there is a possibility the compress operation can delete a state which it believes is a leaf state that is not referenced by any versions, does not have a state lock and is not a parent state of any other states.
The compress operation and the delete state operation now validates when an individual state is deleted that the state is not referenced by any other states (meaning the state being deleted is not a parent state).
This fix has been addressed in the ArcSDE 9.1 General Update Patch 2. See the link below for further instructions.