Jottacloud constantly breaking because of unfixable duplicate files

What is the problem you are having with rclone?

I’m using a crypt remote to upload files to Jottacloud, and I’m regularly running into situations where I get duplicate files on the remote, which completely break the directories they are contained in. A few days ago I uploaded about 12gb of data from a Discord server export with rclone copy, then later exported a few extra channels from the server and ran rclone copy again to upload the remaining files. This resulted in chaos. Instead of just uploading the new files, it kept uploading all the other files too, and by the time I noticed, there were already tens of thousands of duplicates (about 91000 files locally, but over 110000 on the remote). Once I stopped it, I tried running rclone lsf -–recursive in the remote directory, and rclone size, and they both failed with errors like

2025/12/01 22:34:52 NOTICE: Failed to size: couldn't list files: invalid result from listStream: expected[...]

All I could do to try and fix it was purge the directory, empty the trash, and reupload everything. So, I did that today with rclone sync, and it mostly worked, except right at the end, it printed this:

2025/12/03 14:09:08 ERROR : [file name]: Failed to copy: HTTP error 421 (421 Misdirected Request) returned body: "{\"code\":421,\"message\":null,\"cause\":\"\",\"error_id\":\"CorruptUploadOpenApiException\",\"x-id\":\"985400156111\"}"
2025/12/03 14:09:28 ERROR : [file name]: Failed to copy: HTTP error 421 (421 Misdirected Request) returned body: "{\"code\":421,\"message\":null,\"cause\":\"\",\"error_id\":\"CorruptUploadOpenApiException\",\"x-id\":\"186841736168\"}"
[lots more of the above errors]
2025/12/03 14:22:03 ERROR : Encrypted drive 'crypt-base32768:[path]': not deleting files as there were IO errors
2025/12/03 14:22:03 ERROR : Encrypted drive 'crypt-base32768:[path]': not deleting directories as there were IO errors
2025/12/03 14:22:03 ERROR : Attempt 1/3 failed with 21 errors and: HTTP error 421 (421 Misdirected Request) returned body: "{\"code\":421,\"message\":null,\"cause\":\"\",\"error_id\":\"CorruptUploadOpenApiException\",\"x-id\":\"186841736168\"}"
2025/12/03 14:22:03 NOTICE: [path]: Duplicate directory found in destination - ignoring
2025/12/03 14:22:03 NOTICE: [path]: Duplicate directory found in destination - ignoring
2025/12/03 14:22:03 NOTICE: [path]: Duplicate directory found in destination - ignoring
2025/12/03 14:22:03 NOTICE: [path]: Duplicate directory found in destination - ignoring
2025/12/03 14:27:16 ERROR : Attempt 2/3 succeeded
Transferred:       14.305 GiB / 14.305 GiB, 100%, 247.769 KiB/s, ETA 0s
Checks:             91240 / 91240, 100%, Listed 274951
Transferred:        91261 / 91261, 100%
Elapsed time:   17h3m21.1s

4 duplicate directories. Now again, when I run rclone lsf or rclone size, I get this:

ben@archlinux:~$ rclone size crypt-base32768:[path]
2025/12/04 01:06:59 NOTICE: Failed to size: couldn't list files: invalid result from listStream: expected[jottacloud.stats{Folders:401, Files:91261}] != actual[jottacloud.stats{Folders:397, Files:91261}]

Running rclone lsf on the unencrypted remote confirms that there are actually, somehow, duplicate directories with the same name as each other:

ben@archlinux:~$ rclone lsf "jotta:/encrypted-base32768/䎜Ꮃ┭潧⩐矂瓝捳啟/夤⥥卮◘縑鋺蔥戚棪麔㻓诏寃嵦焕袶伈ʟ/䆵捳宲ᖯ䐗摗䌡䀖㴿/圤摌㫉㱠吴䵾┦訯㚒尋臔鶥孽檯䷍剔牗ɟ/碋驳⏊憖⫿浻鄹薘㤿"
㓸燸爌瀬镑睂椄紎䲿/
㓸燸爌瀬镑睂椄紎䲿/
䃜颼逫漲呖膉緥得磟/
䃜颼逫漲呖膉緥得磟/
槎⋖燭輈揀縠醨顮䚿/
槎⋖燭輈揀縠醨顮䚿/
禵鳂瑕点薥绎镼玉ᅟ/
禵鳂瑕点薥绎镼玉ᅟ/

The official jotta-cli tool also lists the same duplicate directories.

rclone dedupe doesn’t help either, it just tells me that it’s not possible for there to be duplicate names:

2025/12/04 02:50:04 NOTICE: Encrypted drive 'crypt-base32768:[path]': Can't have duplicate names here. Perhaps you wanted --by-hash ? Continuing anyway.
2025/12/04 02:50:30 NOTICE: Failed to dedupe: find duplicate dirs: couldn't list files: invalid result from listStream: expected[jottacloud.stats{Folders:401, Files:91261}] != actual[jottacloud.stats{Folders:397, Files:91261}]

Is there any actual way to fix this or prevent it from happening, or is Jottacloud just broken and unreliable?

Run the command 'rclone version' and share the full output of the command.

rclone v1.72.0
- os/version: arch (64 bit)
- os/kernel: 6.12.58-1-lts (x86_64)
- os/type: linux
- os/arch: amd64
- go/version: go1.25.4 X:nodwarf5
- go/linking: dynamic
- go/tags: none

Which cloud storage system are you using? (eg Google Drive)

Jottacloud

The command you were trying to run (eg rclone copy /tmp remote:tmp)

rclone sync [path] crypt-base32768:[path] --backup-dir crypt-base32768:/backup-deleted/[path] --progress --transfers 8 --bwlimit 256K:256K

rclone size crypt-base32768:[path]

Please run 'rclone config redacted' and share the full output. If you get command not found, please make sure to update rclone.

[crypt-base32768]
type = crypt
remote = jotta:/encrypted-base32768
password = XXX
password2 = XXX
server_side_across_configs = true
filename_encoding = base32768

[jotta]
type = jottacloud
configVersion = 1
client_id = XXX
client_secret = 
tokenURL = https://id.jottacloud.com/auth/realms/jottacloud/protocol/openid-connect/token
token = XXX
device = 
mountpoint = 

A log from the command that you were trying to run with the -vv flag

ben@archlinux:~$ rclone size crypt-base32768:[path] -vv
2025/12/04 02:44:49 DEBUG : rclone: Version "v1.72.0" starting with parameters ["rclone" "size" "crypt-base32768:[path]" "-vv"]
2025/12/04 02:44:49 DEBUG : Creating backend with remote "crypt-base32768:[path]"
2025/12/04 02:44:49 DEBUG : Using config file from "/home/ben/.config/rclone/rclone.conf"
2025/12/04 02:44:49 DEBUG : Creating backend with remote "jotta:/encrypted-base32768/䎜Ꮃ┭潧⩐矂瓝捳啟/夤⥥卮◘縑鋺蔥戚棪麔㻓诏寃嵦焕袶伈ʟ/䆵捳宲ᖯ䐗摗䌡䀖㴿/圤摌㫉㱠吴䵾┦訯㚒尋臔鶥孽檯䷍剔牗ɟ "
2025/12/04 02:44:50 DEBUG : fs cache: renaming cache item "jotta:/encrypted-base32768/䎜Ꮃ┭潧⩐矂瓝捳啟/夤⥥卮◘縑鋺蔥戚棪麔㻓诏寃嵦焕袶伈ʟ/䆵捳宲ᖯ䐗摗䌡䀖㴿/圤摌㫉㱠吴䵾┦訯㚒尋臔鶥孽檯䷍剔牗ɟ " to be canonical "jotta:encrypted-base32768/䎜Ꮃ┭潧⩐矂瓝捳啟/夤⥥卮◘縑鋺蔥戚棪麔㻓诏寃嵦焕袶伈ʟ/䆵捳宲ᖯ䐗摗䌡䀖㴿/圤摌㫉㱠吴䵾┦訯㚒尋臔鶥孽檯䷍剔牗ɟ "
2025/12/04 02:44:50 DEBUG : fs cache: switching user supplied name "jotta:/encrypted-base32768/䎜Ꮃ┭潧⩐矂瓝捳啟/夤⥥卮◘縑鋺蔥戚棪麔㻓诏寃嵦焕袶伈ʟ/䆵捳宲ᖯ䐗摗䌡䀖㴿/圤摌㫉㱠吴䵾┦訯㚒尋臔鶥孽檯䷍剔牗ɟ
" for canonical name "jotta:encrypted-base32768/䎜Ꮃ┭潧⩐矂瓝捳啟/夤⥥卮◘縑鋺蔥戚棪麔㻓诏寃嵦焕袶伈ʟ/䆵捳宲ᖯ䐗摗䌡䀖㴿/圤摌㫉㱠吴䵾┦訯㚒尋臔鶥孽檯䷍剔牗ɟ "
2025/12/04 02:45:20 DEBUG : 7 go routines active
2025/12/04 02:45:20 NOTICE: Failed to size: couldn't list files: invalid result from listStream: expected[jottacloud.stats{Folders:401, Files:91261}] != actual[jottacloud.stats{Folders:397, Files:91261}]
ben@archlinux:~$ rclone dedupe interactive crypt-base32768:[path] --dry-run -vv
2025/12/04 02:50:56 DEBUG : rclone: Version "v1.72.0" starting with parameters ["rclone" "dedupe" "interactive" "crypt-base32768:[path]" "--dry-run" "-vv"]
2025/12/04 02:50:56 DEBUG : Creating backend with remote "crypt-base32768:[path]"
2025/12/04 02:50:56 DEBUG : Using config file from "/home/ben/.config/rclone/rclone.conf"
2025/12/04 02:50:56 DEBUG : Creating backend with remote "jotta:/encrypted-base32768/䎜Ꮃ┭潧⩐矂瓝捳啟/夤⥥卮◘縑鋺蔥戚棪麔㻓诏寃嵦焕袶伈ʟ/䆵捳宲ᖯ䐗摗䌡䀖㴿/圤摌㫉㱠吴䵾┦訯㚒尋臔鶥孽檯䷍剔牗ɟ "
2025/12/04 02:50:56 DEBUG : fs cache: renaming cache item "jotta:/encrypted-base32768/䎜Ꮃ┭潧⩐矂瓝捳啟/夤⥥卮◘縑鋺蔥戚棪麔㻓诏寃嵦焕袶伈ʟ/䆵捳宲ᖯ䐗摗䌡䀖㴿/圤摌㫉㱠吴䵾┦訯㚒尋臔鶥孽檯䷍剔牗ɟ " to be canonical "jotta:encrypted-base32768/䎜Ꮃ┭潧⩐矂瓝捳啟/夤⥥卮◘縑鋺蔥戚棪麔㻓诏寃嵦焕袶伈ʟ/䆵捳宲ᖯ䐗摗䌡䀖㴿/圤摌㫉㱠吴䵾┦訯㚒尋臔鶥孽檯䷍剔牗ɟ "
2025/12/04 02:50:56 DEBUG : fs cache: switching user supplied name "jotta:/encrypted-base32768/䎜Ꮃ┭潧⩐矂瓝捳啟/夤⥥卮◘縑鋺蔥戚棪麔㻓诏寃嵦焕袶伈ʟ/䆵捳宲ᖯ䐗摗䌡䀖㴿/圤摌㫉㱠吴䵾┦訯㚒尋臔鶥孽檯䷍剔牗ɟ
" for canonical name "jotta:encrypted-base32768/䎜Ꮃ┭潧⩐矂瓝捳啟/夤⥥卮◘縑鋺蔥戚棪麔㻓诏寃嵦焕袶伈ʟ/䆵捳宲ᖯ䐗摗䌡䀖㴿/圤摌㫉㱠吴䵾┦訯㚒尋臔鶥孽檯䷍剔牗ɟ "
2025/12/04 02:50:56 NOTICE: Encrypted drive 'crypt-base32768:[path]': Can't have duplicate names here. Perhaps you wanted --by-hash ? Continuing anyway.
2025/12/04 02:50:56 INFO  : Encrypted drive 'crypt-base32768:[path]': Looking for duplicate names using interactive mode.
2025/12/04 02:51:20 DEBUG : 9 go routines active
2025/12/04 02:51:20 NOTICE: Failed to dedupe: find duplicate dirs: couldn't list files: invalid result from listStream: expected[jottacloud.stats{Folders:401, Files:91261}] != actual[jottacloud.stats{Folders:397, Files:91261}]

Because you should run in on underlying remote:

rclone dedupe jotta:/encrypted-base32768

and it looks like you run:

rclone dedupe crypt-base32768:

As for the rest of your issues I am not very familiar with jotta. Maybe othe its users can give you some advice.

It can be run on wrapping backends (e.g. crypt)


the issue is a bit confusing.
as per debug logs the issue is Duplicate directory
but according to https://rclone.org/overview/, there is only mention of not supporting duplicate files. no mention about directories?

I forgot to mention that I also tried that and it failed with the same error:

ben@archlinux:~$ rclone dedupe interactive jotta:/encrypted-base32768 --dry-run
2025/12/04 20:01:42 NOTICE: jottacloud root 'encrypted-base32768': Can't have duplicate names here. Perhaps you wanted --by-hash ? Continuing anyway.
2025/12/04 20:04:23 NOTICE: Failed to dedupe: find duplicate dirs: couldn't list files: invalid result from listStream: expected[jottacloud.stats{Folders:141502, Files:314828}] != actual[jottacloud.stats{Folders:141498, Files:314828}]

@albertony, i think you are a jottacloud user?
if so, any insight into this topic?

Same issue here. JottaCloud whitelabel. In addition it keeps uploading same files over and over.

EDIT: Could seem to be rar2fs is the issue. It seems like it serves (some of the files for some reason) in a way that gives different md5 sums.