Some poking around with SQLite Manager shows they are still listed in moz_places table in places.sqlite - it's the moz_bookmarks table got reset to default.
Oddly, keyword entry still works. Not only that, when the keyword is typed in full, the site for the keyword is offered in the dropdown that comes up, along with its favicon. That's despite having history already cleared and not visiting the site since.
Is this a known bug? How to prevent my bookmarks being half-eaten?
Ignore the UA string you see below, I'm not posting from 2.48. Go by this one instead -
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Mozilla/5.0 (X11; Linux x86_64; rv:51.0) Gecko/20161201 SeaMonkey/2.48b