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When you dispute with the CRAs they have to notify the furnisher of the information. It is possible the furnisher deleted it from EX because they could not verify its accuracy.
Any item removed due to a dispute can be re-inserted if the furnisher provides verification of the debt. Or anyone trying to re-insert it for that matter. As long as they can prove to the CRA it is a valid account.
No, the CRA could delete also.
The Beacon 5 is the same as from here, also known as FICO04.