Firefox has deleted my bookmarks, and the restore procedure doesn't work, nor does trying to overwrite the ones on my PC from Sync.
The bookmarks appear to have disappeared as I was creating a bookmark.
I tried restoring from every restore point listed in "Import and Restore", and they all appear to be empty.
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Did you check the file size of the JSON backups in the bookmarkbackups folder to see if any is large enough to contain the bookmarks?
Problems with bookmarks and history not working properly can be caused by a corrupted places.sqlite database file.
You can check for problems with the places.sqlite database file in the Firefox Profile Folder.
All of my bookmarks files (.json) are 1kb, including all restore points going back to November 2012 in the bookmarkbackups folder.
I ran the Places Maintenance add-on and it didn't flag anything, though it appeared to compact the places.sqlite file by 50%. Its size is now 10mb. That file is not set to read-only.