Apple Books says imported PDF is now damaged

Apple Books cannot open a PDF I had imported saying PDF is damaged.

The Issue:

I had “Apple Books” corrupt a PDF I’d been working with for over three years - I’d been notating and marking up the PDF across my devices.

All of a sudden (Sept 2024, iPad & Mac OS Sonoma), I got the error “PDF damaged” on my iPad - and because of how well Apple sync’s across its devices this corruption spread to the version stored on iCloud and to every other device.

The Fix:

Restore a version of the PDF from my Time Machine Backup. The only problem was trying to find where “Apple Books” stored my freaking PDF. After quite a bit of digging around, I think the mythical “iCloud Drive/Books” folder is an Apple internal thing and for us mere mortals, this is how we get to it..

Details

First, a sanity check from Terminal (or Finder > Go > Go  To Folder):

$ cd ~/Library/"Mobile Documents"/iCloud~com~apple~iBooks/Documents
// check that the PDF actually exists and cannot be opened by Preview (“damaged PDF” error)

Next, try to ‘Restore’ from Time Machine:

1. "Time Machine" > "Browse Time Machine Backups" and follow along to the right ‘Documents’ folder

2. Navigate to place where "Apple Books" stores its Documents

a) ~/Library/"Mobile Documents" => Note that this gets referred to as the “iCloud Drive” at this point

b) iCloud~com~apple~iBooks => this is now the mythical “iCloud Drive/Books”  - for me, this folder was grayed out..

c) Documents => hopefully, you see all your PDFs from “Apple Books” here

3. Select the file that was corrupted by “Apple Books”

- Check that this backup version of the file is OK by opening it / ‘quick look’

- If OK, select the file and press the “Restore” button

- In my case, at this point, there was no indication that anything was happening. 

- I waited for a few minutes, it looked as if the system was frozen..

- I pressed Cmd+Option+Esc, and it immediately put me back to my desktop as I was before going into Time Machine

- I checked in Terminal again, and I saw that the file had been restored..

4. If “Restore” doesn’t seem to work. Another way I tried (seems more reliable..)

- After checking the Time Machine version was OK

- ‘Copy’ the file I wanted restored (Rt Click > Copy)

- ‘Paste’ file somewhere 

- “Delete” damaged PDF from “Apple Books”

- Import’ the recovered and pasted file into “Apple Books”

Hopefully, it is sorted out at this stage.

Good luck!