The data is stored in the intersection even when the parent is removed.
To clear the data, you would need to put the children back under the parent, run a DM job to clear data that is for E#[YourTopParent].DescendantsInclusive and T#[YourApplicableYear].DescendantsInclusive and then force consolidate.
This will clear the elimination data for the parent (but also the data for the children entities).
Then, the parents can be deleted/removed as needed.
Note: There is a pending update to the product to address this in a future release.