Workflow: Migrate All CherryTree Notes to Joplin Server – Part 2

In Part 1 I planned the move from CherryTree to Joplin, built a converter, proved it didn’t lose anything, set up my own sync server at home, and got a two-notebook pilot running on my tablets. This is Part 2: how I moved the other 40,000 notes, what broke along the way, and how I decided what not to move.

Where it ended up

1. Move in batches, newest first

After the pilot I could have moved everything in one overnight run. Instead I sorted my notebooks by when I last edited them and moved them in batches:

Why newest first? The notes I was actively studying reached my tablets within an hour. If something had gone wrong, it would have shown up on a small batch I knew well, not halfway through 40,000 notes. And each batch taught me something that made the next one smoother.

Every batch followed the same loop: list → convert → check → import → upload → verify → archive. Same steps each time, so nothing got skipped.

2. Do the heavy lifting on the fast machine

In the pilot, the home server’s old hard drive took 40 minutes for 1,800 notes. So for the real batches I imported on my desktop, which has a fast SSD, and let sync carry everything up to the server. Batch 2 (5,200 notes) took 8 minutes to import and 13 to upload, about three times as many notes in half the time.

Joplin’s desktop app also surprised me in a good way: it reads the text inside pictures (OCR) and syncs it. Thousands of screenshots of slides and terminal output became searchable on my tablets without me doing anything.

3. The 88 pictures that didn’t make it

After the biggest batch, the totals were off: notes matched exactly, but attachments were 36 short. Digging in, I found 12 notes from several batches whose pictures had never been attached. Joplin had imported the text but left each picture as a link to a file on my desktop. On the tablets they would have been broken images. Joplin’s log showed no errors, and the same notes imported perfectly in testing.

The fix was simple once found: re-import those 12 notes, check that every picture attached, and only then move the broken copies to Joplin’s trash. All 12 worked the second time.

import re, sqlite3
db = sqlite3.connect("file:database.sqlite?mode=ro", uri=True)
local = re.compile(r"![[^\]]*\]\((?!:/|https?:|data:)[^)]+\)")
bad = [t for t, b in db.execute(
        "select title, body from notes where deleted_time = 0") if local.search(b)]
print(len(bad), "notes with unattached images")

4. Archive and freeze the originals

After each batch I moved the converted CherryTree notebooks into one archive folder in my git repository, using git mv so their history follows them. When everything was done, I made that folder read-only. CherryTree can still open an old notebook to look something up, but it can’t save, so nobody (me included) can accidentally edit a copy that’s no longer the real one.

5. Deciding what not to move

The last few notebooks were the personal ones I’d protected with a password in CherryTree. Joplin has no per-notebook passwords: once imported, a note opens on any device signed in to my account. Joplin can encrypt everything end to end, and the tablet app can be locked with biometrics, but nothing gives the same “this notebook needs its own password” feeling.

So I made a decision instead of a workaround: those few notebooks stay in CherryTree, password-protected, and I only open them on my computers. Everything else lives in Joplin.

While checking them I noticed two of the protected notebooks had exactly the same number of notes and pictures. Comparing them note by note showed an exact duplicate, saved under a different password. Every note and every picture matched. I kept one and deleted the other, which git history still keeps.

used = set()
for d, _, files in os.walk(export_dir):
    for f in files:
        if f.endswith(".md"):
            text = open(os.path.join(d, f), encoding="utf-8").read()
            used |= {os.path.basename(unquote(m))
                     for m in re.findall(r"_resources/([^)\s\"'>]+)", text)}
for f in os.listdir(resources_dir):
    if f not in used:
        os.remove(os.path.join(resources_dir, f))

6. Where everything lives now

• Joplin on two tablets and the desktop: all my everyday notes, synced through my home server over a private network.
• A nightly backup of the server, copied to a second machine, plus a readable Markdown copy of every note in git, minus the private notebooks.
• CherryTree on my computers only, for a few password-protected notebooks.
• A read-only archive of all the original CherryTree notebooks, with full history.

What I’d tell you before your own move

• ☐ Move in batches, starting with the notes you use most.
• ☐ Do imports on your fastest machine; let sync do the uploading.
• ☐ Count notes and attachments before and after every batch.
• ☐ Check specifically for pictures that didn’t attach.
• ☐ Archive the originals as you go, then lock them read-only.
• ☐ Decide which notes need stronger protection than your new app offers, and leave those where they’re safe.
• ☐ Delete readable copies of private notes as soon as you’re done with them.
• ☐ Keep your backups, and test restoring them.