Inksky
E-readers last for years, but the books and highlights on them are fragile. A corrupted database, a lost device, or a factory reset can wipe out years of reading history in seconds. Cloud sync helps, but it’s not a backup — and each platform handles it differently. Here’s how to protect your library and annotations across Kindle, Kobo, and Boox.
Kindle: convenient but incomplete
Amazon’s Whispersync is the gold standard for convenience. Your purchased books, reading position, highlights, and notes sync automatically across every Kindle device and app. Pick up your phone where you left off on your Paperwhite — it just works.
What’s backed up: Books purchased from Amazon, reading progress, highlights, notes, bookmarks, and Goodreads integration data. Everything lives in Amazon’s cloud and survives a device reset or upgrade.
What’s NOT backed up: Sideloaded books and their annotations. If you transfer a book via USB or Send-to-Kindle (as a personal document), highlights and notes are device-local. They survive if you use Send-to-Kindle (they sync across devices signed into the same account), but USB-sideloaded annotations are lost if the device is reset.
The gap: Amazon doesn’t give you a way to bulk-export all your highlights. You can export highlights from a single book via the Kindle app or the web notebook, but there’s no “download everything” button. If you want a complete archive, you’ll need a third-party tool.
Kobo: sync with gaps
Kobo devices sync purchased books, reading progress, and bookmarks through your Kobo account. Highlights and annotations from Kobo Store books sync as well. The sync is reliable for store purchases, and Kobo’s partnership with Pocket means you can save articles from the web and read them on your device.
What’s NOT backed up: Sideloaded books (even KEPUBs) and their annotations. Kobo’s cloud only covers purchases from the Kobo Store. If most of your library is sideloaded, Kobo’s sync provides almost no protection.
The workaround: Kobo devices expose their database file (.kobo/KoboReader.sqlite) when connected via USB. You can copy this file to your computer as a manual backup. The Kobo Utilities Calibre plugin can automate this — set it to back up the reading database every time you connect.
Boox: you’re on your own
Boox devices run Android with no centralized cloud service for reading data. The built-in Boox cloud sync handles notes from the Notes app, but reading progress, highlights, and annotations in NeoReader or third-party apps live entirely on the device.
The upside: You control everything. Set up folder sync with Dropbox, Google Drive, or OneDrive using a file sync app like FolderSync or AutoSync. Your entire ebook folder and annotations can mirror to the cloud automatically.
The downside: You have to set it up. Boox doesn’t do it for you, and a factory reset without a manual backup means starting over.
Calibre: your offline backup strategy
Calibre on your computer is the most reliable backup for any e-reader ecosystem. Here’s a setup that covers everything:
- Maintain a master Calibre library on your computer with every ebook you own, properly formatted and metadata-clean.
- Back up the Calibre library folder to an external drive and/or cloud storage (the metadata.db file and the book folders together form a complete backup).
- Use the Kobo Utilities plugin (for Kobo users) to back up reading progress and annotations each time you connect.
- Use the Annotations plugin to fetch highlights from Kindle and Kobo devices and store them as custom columns in Calibre.
This gives you a complete, platform-independent backup of your library, metadata, and reading history. If you switch from Kindle to Kobo or vice versa, you can rebuild from Calibre without losing anything.
Exporting highlights to Readwise and Notion
Readwise integrates with Kindle and Kobo to automatically pull in your highlights and sync them to Notion, Obsidian, Roam Research, and other note-taking apps. It’s a paid service ($7.99/month) but eliminates the manual export step entirely. For heavy highlighters, it’s worth it — your Kindle highlights appear in your Notion database the next day without any effort.
For Boox users, Readwise doesn’t have direct integration, but you can export highlights manually from NeoReader or use KOReader with its built-in export options, then import the file into Readwise.
If you prefer not to pay for Readwise, the free approach: export highlights from each device as a text file (Kindle’s email export, Kobo’s annotation file via USB, Boox’s export-to-TXT), save them in a folder synced to your cloud storage, and search them when needed.
A backup checklist
Run through this once, then you can mostly forget about it:
- Set up Calibre with your complete library on a computer.
- Back up the Calibre library folder to an external drive monthly.
- Enable Kindle/Kobo cloud sync for purchased books.
- For sideloaded books, use Send-to-Kindle (Kindle) or Kobo Utilities backup (Kobo).
- Set up Readwise (or a manual export routine) for highlights.
- For Boox, configure a folder sync app for your ebook directory.
Your future self, holding a new e-reader and wondering where all those highlights went, will thank you.