Is this file server a domain member, or is it a standalone server in a workgroup? NTFS file permissions use SIDs (security identifiers) to reference users and groups.
In a workgroup environment, the SIDs are defined on the fileserver itself, as part of the local users and groups configured on that server. If you are wiping out the boot disk and installing a new operating system entirely, then the permissions will reference SIDs that no longer exist, so you'll need to reset all of the permissions. But if you're just doing an upgrade, that won't affect the local users and groups so the permissions will remain intact.
In a domain environment, the SIDs for domain users are defined on the domain controllers. So even if you wipe out the boot drive and reinstall a new operating system, the files on your data drive are still using the same SIDs, and they are still defined by your domain controllers, so the permissions are totally perserved.