Clonebox Manual

Clonebox is a USB management tool built specifically for DJs. It solves one problem: keeping multiple USB drives in sync, verified, and CDJ-ready — without the hassle of re-exporting your entire library every time something changes.

Clonebox works entirely offline. Your music never leaves your computer. No accounts, no cloud, no subscriptions.

What Clonebox is for

• ·Keeping a backup USB in sync with your main USB
• ·Syncing cue points and ratings you set on the CDJ back to all your drives
• ·Verifying that copied files are byte-for-byte identical (no silent corruption)
• ·Preparing a new blank USB for CDJ use (FAT32, CDJ-ready format)
• ·Finding and removing duplicate tracks to free up space
• ·Removing macOS junk files that waste space on your USB

What Clonebox is not

• ·Not a general-purpose backup tool — it is optimised for DJ USBs and intentionally skips macOS/Windows system files
• ·Not a music player or organiser — use Rekordbox for preparing your library
• ·Not a replacement for Rekordbox — it works alongside it

When you open Clonebox, plug in your USB drives. Clonebox automatically detects all connected drives and displays them in the drive selector.

Source (A) and Destination (B)

Most operations work with two drives: a Source (A) and a Destination (B). Select each from the dropdowns. The drive cards show:

• ·Drive name and path
• ·Filesystem type (FAT32, exFAT, NTFS) — shown in green if CDJ-compatible, red if not
• ·Total size and free space
• ·Whether a Rekordbox database (PIONEER folder) was detected
• ·Number of files found after scanning

Single drive operations

Some features (Duplicate Finder, Free Up Space) work on a single drive. Select only Source (A) and use the buttons that appear below the drive card.

Diff & Sync is the core feature of Clonebox. It scans both drives, compares every file, and shows you exactly what is different — without copying anything yet.

How it works

1. Select Source (A) and Destination (B)
2. Click Diff & Sync — Clonebox scans both drives simultaneously and compares every file by name, path, and size
3. Click View Result → to open the diff screen
4. Review the differences and choose what to copy
5. Click Check & Copy → — a confirmation screen shows exactly what will happen before anything is written

What the diff screen shows

• ·Only on A — files present on A that are missing from B. Select all or individually to copy to B.
• ·Only on B — files present on B that are missing from A. Default: not selected (to avoid overwriting your main).
• ·Conflicts — files with the same name on both drives but different content. Audio conflicts may indicate corruption. Rekordbox conflicts (cue points, ratings) are normal.
• ·Identical — files that are exactly the same on both drives. Nothing to do.

Sync Rekordbox database

The checkbox Sync Rekordbox database (ratings, cues, playlists) at the bottom is on by default. When enabled, all files in the PIONEER folder are always copied from A to B — even if the diff shows them as identical. This ensures that ratings and cue points you set on the CDJ during a gig are always propagated to your backup drives.

After copying

Every copied file is automatically verified using xxHash. If the hash of the copy does not match the original, Clonebox flags the file and retries once. You see a full report at the end: files copied, files verified, files failed.

Clone copies all files from A to B in one step — without a diff, without deleting anything on B first.

Behaviour

• ·All files from A are copied to B
• ·Files already on B that are NOT on A are left untouched
• ·Files on both drives are overwritten with A's version
• ·Every copied file is hash-verified after copying

When to use Clone

• ·Moving your collection from one USB to a new, larger one
• ·Filling a backup USB that is currently empty
• ·When you know B has no relevant files of its own and just needs A's content

Wipe & Clone completely erases destination B, formats it, and then copies everything from A. The result is a perfect, clean copy of A on B.

Format options

Before wiping, you choose the filesystem:

• ·FAT32 — works on all Pioneer CDJ models, including older ones. Recommended for maximum compatibility. On Windows, a one-time administrator permission prompt appears.
• ·exFAT — works on newer CDJ models (NXS2, CDJ-3000). No administrator permission required on Windows.

What happens step by step

1. All files on B are deleted
2. B is formatted to FAT32 or exFAT with the correct partition scheme (MBR) for CDJ compatibility
3. All files from A are copied to B
4. Every file is hash-verified

Windows note

When using FAT32 on Windows, a system security prompt (UAC) appears asking for administrator permission to format the drive. This is a standard Windows requirement for disk formatting. Click Yes to proceed.

Sync Rekordbox copies only the Rekordbox metadata from A to B — ratings, cue points, loops, waveforms, and playlists — without re-copying your music files. This takes seconds instead of minutes.

When to use this

You played a set on your CDJs. During the set you:

• ·Set new cue points on a track
• ·Gave tracks a star rating
• ·Moved tracks between playlists

The CDJ wrote these changes back to the PIONEER folder on your USB. Now you want your backup USB to have the same updated data. Click Sync Rekordbox — done in seconds, no music re-copying.

What gets synced

• ·The entire PIONEER folder from A is copied to B
• ·This includes: cue points, hot cues, loops, memory cues, ratings, waveform data, playlist structure
• ·Music files (.mp3, .wav, .flac etc.) are not touched

The Duplicate Finder scans a single drive and finds tracks stored more than once, using hash-based comparison to detect identical content — even if the filenames are different.

How to run it

1. Select a drive as Source (A)
2. Click Scan this drive in the drive card, or use the Duplicates button after scanning
3. Choose whether to enable Hash check (recommended)
4. Click Scan for duplicates

Hash check

With hash check enabled, Clonebox reads every audio file and computes a fingerprint. Two files with the same fingerprint are byte-for-byte identical — even if they have different names or are in different folders. This is the most reliable way to detect true duplicates.

Hash checking a full 256 GB USB can take 5–15 minutes. The progress bar shows which file is being processed.

Results

Duplicates are shown grouped by filename or content. The first copy is marked keep. Additional copies are marked duplicate with a Delete button. You can delete all duplicates at once with Delete all X duplicates.

When macOS accesses a FAT32 or exFAT drive, it silently creates hidden ._filename files alongside every real file. These are "resource fork" sidecar files used by macOS internally. They serve no purpose on a DJ USB and can accumulate to 2–4 GB on a full drive.

How to clean

1. Select the drive to clean as Source (A)
2. Click Clean Up in the drive card
3. Clonebox finds and deletes all ._* files

This is a Mac-only feature. Windows does not create these files.

Each drive card has a Safe Eject button. Clicking it properly dismounts the drive before physical removal, preventing data corruption.

Works for all drive types: USB sticks, external HDDs, and SSDs. On Windows, Clonebox uses the same system call as "Safely Remove Hardware". On Mac, it calls diskutil eject.

After ejection, the drive is automatically removed from the Clonebox drive list.

After a gig: sync CDJ changes to backup

1. Plug in main USB (the one you played with) as A
2. Plug in backup USB as B
3. Click Sync Rekordbox
4. Done — cue points and ratings are on both drives

Adding new tracks: sync only what changed

1. Export new tracks from Rekordbox to your main USB as usual
2. Plug in main USB as A, backup USB as B
3. Click Diff & Sync
4. Only the new tracks and updated Rekordbox data are copied

Setting up a brand new USB

1. Plug in existing USB as A, new blank USB as B
2. Click Wipe & Clone
3. Choose FAT32 (recommended for all CDJ models)
4. Confirm — new USB is formatted and filled automatically

Moving to a bigger USB

1. Plug in old USB as A, new larger USB as B
2. Click Clone
3. Everything from A is copied to B. B now has your full collection plus free space for more.

Merging two USBs that drifted apart

Both USBs get everything the other one has. After syncing, both drives have the complete combined collection.

1. Plug in USB A and USB B
2. Click Diff & Sync
3. In the result screen: select all files under "Only on A" and all files under "Only on B"
4. Click Check & Copy — both drives end up with the complete combined collection

Adding tracks from a second USB to your main USB

You have two separate USBs and want to add tracks from one into the other. The direction does not matter — after scanning you choose per section which way files are copied.

1. Plug in both USBs — it does not matter which is A and which is B
2. Click Diff & Sync
3. In the result screen you see two sections: "Only on A" and "Only on B"
4. Select the tracks you want to add from either section — files under "Only on A" go to B, files under "Only on B" go to A. You can select from both sections at the same time.
5. Enable Sync Rekordbox database to also copy waveform and cue point data for the new tracks
6. Click Check & Copy

The tracks will be playable on your CDJ immediately. Note: they will not appear in your Rekordbox playlists until you re-export from Rekordbox on your computer. Via the CDJ's "All Tracks" browse mode they are immediately accessible.

Does Clonebox work without Rekordbox?

Yes. Clonebox works directly with USB drives. You do not need Rekordbox installed. However, Clonebox is designed to work with USB drives that were prepared with Rekordbox — it preserves the PIONEER folder structure that CDJs need.

Which CDJ models are supported?

Any CDJ or XDJ that reads from USB and uses the Rekordbox PIONEER folder structure. Tested on CDJ-2000NXS2 and CDJ-3000. Should work on all NXS/NXS2/3000 series.

My CDJ shows "Format USB" after Wipe & Clone

This usually means the drive was formatted with the wrong filesystem or partition table. Clonebox formats with FAT32 + MBR, which is the correct format for Pioneer CDJs. If you see this error, try Wipe & Clone again and choose FAT32.

Why does Diff & Sync show "identical" but I know I changed cue points?

Cue point and rating changes in the PIONEER folder sometimes do not change file sizes — only file content. Our diff compares by size, so it may not detect these changes. Use Sync Rekordbox or ensure the Sync Rekordbox database checkbox is enabled in the diff screen.

Can I use Clonebox on Windows and Mac?

Yes. Clonebox is available for both Windows 10+ and macOS 12+. The same USB can be used on both platforms — just plug it in.

What happens if a file fails to copy?

Failed files are listed by name with the exact error. After the operation completes, you can retry just the failed files without re-copying everything that succeeded.

Does Clonebox modify my Rekordbox library on my computer?

No. Clonebox only reads and writes to USB drives. Your Rekordbox library on your computer is never touched.

Can I use exFAT instead of FAT32?

Yes. In Wipe & Clone, you can choose exFAT. exFAT works on newer CDJ models (NXS2, CDJ-3000). FAT32 is recommended for maximum compatibility with all CDJ models including older ones.