I lost most of my data, please help

Help
1

Hello,

I really hope someone can help me. I’ve been using Cloudflare R2 with Cryptomator to store my data, and initially everything worked fine—until I made a mistake.

In Finder (macOS), I renamed the mounted folder from “R2 Encrypted” to “R2_Encrypted”.

I had no idea this would unleash chaos. It triggered a process that lasted nearly two days. Eventually, I gave up and clicked cancel.

Now, I have two folders on Cloudflare R2:

  • R2 Encrypted/
  • R2_Encrypted/

Total size: 100.13 GB

It appears that the data is still there. However, when I unlock the vault using Cryptomator, most of the contents are missing—including irreplaceable childhood photos and pictures of my late father. In hindsight, it was foolish not to have an additional backup, but that’s beside the point.

Earlier today, I copied the data to my local machine in hopes of faster access via Cryptomator, using the following command:

rclone sync “cloudflare-r2:houmie/R2 Encrypted/” ~/Downloads/R2_Encrypted2 --inplace --progress

During the sync, I received many errors of this nature:

2025/07/04 13:23:52 ERROR : d/ZW/XW4I273H2GPE6F4OO3HUNJTAY46P75/: Failed to copy: open /Users/houmie/Downloads/R2_Encrypted2/d/ZW/XW4I273H2GPE6F4OO3HUNJTAY46P75: is a directory
2025/07/04 13:23:52 ERROR : d/ZX/RX5ICCNVBAQEL5NICOGCDWQN6QQM4Z/: Failed to copy: open /Users/houmie/Downloads/R2_Encrypted2/d/ZX/RX5ICCNVBAQEL5NICOGCDWQN6QQM4Z: is a directory
2025/07/04 13:23:52 ERROR : d/ZV/O444SU7PZG5URDQXCRI4NIEXBVMVIP/NaYdEFJBPfjKwhoEiJPX5d-SZHBvKQ==.c9r/dir.c9r: Failed to copy: mkdir /Users/houmie/Downloads/R2_Encrypted2/d/ZV/O444SU7PZG5URDQXCRI4NIEXBVMVIP: not a directory
2025/07/04 13:23:53 ERROR : d/ZZ/YPMUNONF74AQC5WLKIQJWCXVYJLCVW/: Failed to copy: open /Users/houmie/Downloads/R2_Encrypted2/d/ZZ/YPMUNONF74AQC5WLKIQJWCXVYJLCVW: is a directory
2025/07/04 13:23:53 ERROR : d/ZV/O444SU7PZG5URDQXCRI4NIEXBVMVIP/ymDZ4q2owZ-xRS-lEJxqivDXdZ8=.c9r/dir.c9r: Failed to copy: mkdir /Users/houmie/Downloads/R2_Encrypted2/d/ZV/O444SU7PZG5URDQXCRI4NIEXBVMVIP: not a directory
2025/07/04 13:23:55 ERROR : d/ZO/NTL6SR4TUGX5MHFWSSMIJGXWOCNQN4/: Failed to copy: open /Users/houmie/Downloads/R2_Encrypted2/d/ZO/NTL6SR4TUGX5MHFWSSMIJGXWOCNQN4: is a directory
2025/07/04 13:26:22 ERROR : Local file system at /Users/houmie/Downloads/R2_Encrypted2: not deleting files as there were IO errors
2025/07/04 13:26:22 ERROR : Local file system at /Users/houmie/Downloads/R2_Encrypted2: not deleting directories as there were IO errors
2025/07/04 13:26:22 ERROR : Attempt 3/3 failed with 3194 errors and: open /Users/houmie/Downloads/R2_Encrypted2/d/ZO/NTL6SR4TUGX5MHFWSSMIJGXWOCNQN4: is a directory
Transferred:   	   87.991 GiB / 87.991 GiB, 100%, 0 B/s, ETA -
Errors:              3194 (retrying may help)
Checks:             75742 / 75742, 100%, Listed 225114
Transferred:        40865 / 40865, 100%
Elapsed time:    2h18m5.2s
2025/07/04 13:26:22 NOTICE: Failed to sync with 3194 errors: last error was: open /Users/houmie/Downloads/R2_Encrypted2/d/ZO/NTL6SR4TUGX5MHFWSSMIJGXWOCNQN4: is a directory

After unlocking the folder with Cryptomator, I can only see about 25 MB of data, even though I transferred approximately 88 GB.

Is there any way to recover the missing files or restore the vault to a usable state?

Any advice would be deeply appreciated.

Kind regards,
Houman

2

Mhm,

Combining both folders without rclone should work, because I assume that both files together hold all the data.
What I would try:

  1. Download both folders from cloudflare to your local system (make sure really every file and folder is local and thers no sync issue)
  2. make a backup of your downloaded mess so you can go back
  3. Move everything from “R2_Encrypted” to “R2 Encrypted”
  4. remove vault “R2 Encrypted” (on cloudflaire) from the app.
  5. Add local vault “R2 Encrypted” to the app and open
3

Hi Michael,

Thank you for your reply.

That’s a good idea. However, I’m not quite sure how to copy everything over from R2 efficiently. Cloudflare’s R2 essentially behaves like AWS S3—it doesn’t allow me to download from the root directory directly. I would need to download each file individually and manually recreate the directory structure, which is both tedious and error-prone.

Is there any tool you would recommend that can download the files exactly as they are, without trying to interpret or process them?

Best regards,
Houman

4

I do not use cloudflaire R2 so I do not have a recommendation.
Maybe anyone else?