File system sync - Help! - unencrypted notes still present in sync dir after re-encryption

Operating system


Joplin version


Desktop version info

Joplin 2.14.22 (prod, darwin)

Client ID: 0dfa35f10191400fb20c5140837ca26f
Sync Version: 3
Profile Version: 46
Keychain Supported: Yes

Revision: e579eb9

Backup: 1.4.1
Better Code Blocks: 1.1.0
Combine notes: 1.2.2
Conflict Resolution: 1.2.3
Csv Import: 1.0.1
Jarvis: 0.8.2
Markdown table calculations: 1.0.5
Markdown Table: Sortable: 1.2.2
Note overview: 1.7.1
Paragraph Extractor: 1.1.2
Quick Move: 1.1.0
Rich Markdown: 0.15.0
Tagging: 1.0.3

Sync target

File system


Markdown Editor

What issue do you have?

I have recently decided to encrypt all my notes.

Steps taken:

  1. In Preferences > Synchronization > Encryption I enabled encryption and created Master password.
  2. In Preferences > Synchronization > Encryption > Advanced Settings I selected Re-encrypt data, so that all my previous notes are encrypted.
  3. I selected it on one device only and let it run. I turned Joplin off and turned it back on during the process as there was no indicator in GUI the encryption was going on.
  4. I observed other devices syncing notes via Syncthing.

Intended result:
All my notes in my filesystem sync target directory (~/Joplin) are encrypted.

Actual result:
Some notes are encrypted and some are unecrypted. How do I know? I checked the directory with grep -r -n "encryption_applied: 1" . and grep -r -n "encryption_applied: 0" . and received many hits for both.

What did I do wrong? Did I stopped the re-encryption by turning the Joplin off and back on in the process?

I let the re-encryption run again over night without any disruptions. In the morning, I still have 2924 unencrypted .md and 2736 encrypted .md files on my filesystem sync directory.

This means that the issue is reproducible on my machine.

The re-encrypt function fails to encrypt old notes on filesystem sync.

Is there anyone more familiar with Joplin encryption who could shed some light?

Maybe it is related with the Note History?

1 Like

Of course. The unencrypted .md files are note changes, not full notes.

However, I thought re-encryption encrypts everything.

Do I have to throw away note history? I thought all the files are basically just changes to notes, that is there is no single complete note in my filesystem target sync directory, just a series of changes.