WHM Backup Configuration: Incremental vs Compressed for Large Datasets

Answering the Core Question

When WHM is set to Incremental, the backup engine builds a directory tree on the same filesystem as the account data. Unchanged files are hard‑linked to the previous snapshot, keeping the local footprint small and the backup run fast.

During the transport step the engine simply copies that tree to the chosen destination. If the destination filesystem does not understand or preserve hard links (which is the case for most S3‑compatible buckets, SFTP servers, and many network shares), each file is treated as a separate object. The result is that the upload size equals the full size of the snapshot, not the reduced size of the hard‑linked tree. Uploading many small objects also increases request costs on object stores.

Does WHM Flatten Incrementals into Portable Archives?

No. WHM does not automatically create a tarball from an incremental snapshot during the transport phase. Flattening occurs only when either of the following is true:

• The destination’s Compress Backups toggle is enabled. In that case WHM packages the entire tree into a single .tar.gz before sending.
• A separate Transfer System Backups job runs after the backup completes, which can also create a compressed archive.

If neither condition is met, the engine copies the hard‑linked tree as‑is.

Practical Verification Steps

1. Check Backup Type – In WHM, navigate to Backup Configuration > Backup Type and confirm whether Incremental is selected.
2. Inspect Destination Settings – Open the destination you use (S3, SFTP, NFS). Look for the Compress Backups option. If unchecked, the engine will not create a tarball.
3. Run a Test Backup – Execute a manual backup for a single account. After completion, list the remote objects:

   # S3 example
   aws s3 ls s3://my-backup-bucket/2026-10-13/ | wc -l
   # SFTP example
   sftp user@host:/path/to/backups > /dev/null
   

   A large number of individual files indicates that hard links were not preserved.
4. Enable Compression for the Destination – In the destination configuration, check Compress Backups and re‑run the test. Verify that a single .tar.gz file appears.
5. Review the Log – Inspect /usr/local/cpanel/logs/backup_log for entries like Compressing backup for destination or Copying file to confirm the action taken.

Key Takeaway

Incremental backups are space‑efficient locally but lose that advantage when sent to destinations that cannot preserve hard links. To maintain portability and cost‑efficiency for remote storage, enable compression for the destination or use a destination that supports hard links.

Diagnostic Question

What type of remote destination are you targeting (S3, SFTP, NFS, or another object store) and does it preserve hard‑link metadata? Knowing this will help decide whether to keep incremental mode or switch to compressed backups.