Mailbox permissions (full, send as, and send on behalf) are not a value that can be quickly obtained from Microsoft for a given account. There are situations in which that information is needed immediately. As a result, permission data is stored in local storage where it can be queried in a timely and reliable manner.
There are circumstances where the permissions that were recorded locally and those that exist in Office 365 can differ. This can happen for a number of reasons, including but not limited to:
Despite efforts to reduce the occurrences of inconsistent permissions between the local store and what is in Office 365, the issue is still somewhat prevalent. To identify and remediate these inconsistencies, the Permission Repair Tool was created.
The "Reapply" option will always be available for inconsistent permissions. It is the only option for inconsistent "full" and "send as" permissions which are required for linked NetIDs. When "Reapply" is clicked, if the permission is absent in Office 365 but stored locally, it will queue a job to add the permission to Office 365. If the permission is absent locally but present in Office 365, clicking "Reapply" will add the permission to the local store.
The "Remove" option is only possible for inconsistent permissions that aren't provided through linking. If the permission is present locally but not applied to the account in Office 365, clicking "Remove" will delete the permission from the local store. If the permission is present in Office 365 but stored locally, clicking "Remove" will queue a job to remove the permission from Office 365.
Note: The Repair Permissions Tool does not automatically take any action on inconsistent permissions. The user or authorized administrator of the account must click the "Remove" or "Reapply" button the remediate the inconsistent permission(s).