Limiting possible damage to one session is probably ok, since the probability of the damage is
low. So just doing a backup on startup (or, alternatively, restoring from it if the current
copy is mangled too much due to some hardware/kernel failure) would seem fine.
Another solution is to just separate the normal, manually made bookmarks from everything else.
The only real precious stuff is the actual bookmarks, all other automatically collected data
is just a convenience which helps you type less, and which would fix itself over time anyway.
Since they're at rc1 already, maybe it's just too late for all that. I wonder though what
platform they develop on, since this is very obvious stuff and the fact that it is still
present in rc1 probably means Windows is their primary target. I would understand that, but
that's a pity.