- Stop Safari
- Recover bookmarks from backup (from time machine backups, for example)
- Start Safari
- See recovered bookmarks area - SUCCESS!
- See recovered bookmarks area VANISH - uh oh! What went wrong?
iCloud "helpfully" learned about the deleted bookmarks, and successfully removed the recovered bookmarks. Touching the file does not seem to help, nor does creating a new bookmark. Here is a sequence I have been successful with:
Step 1: Shut off iCloud for Safari (in System Preferences, iCloud)
Step 2: Recover the file - ~<your user id>/Library/Safari/Bookmarks.plist
Step 3: Open Safari, Move bookmarks around - I put a group of bookmarks that had been accidentally deleted into a subfolder, and then moved it back
Step 4: Turn on iCloud for Safari
Step 5: Fix what iCloud inevitably does. For example, one of my bookmarks bar items that I had deleted and then followed steps 1-3 on, changed position in the bookmarks bar list. I simply put it back to the right location one last time.
Then it stays, and iCloud has learned what you want. iCloud is not time machine. It does not allow, at the moment, a recovery to what your bookmarks used to be.