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73416ba
(Get the code!)
Jo, the file that I am looking at right now is cookies.sqlite. I have a copy from before clearing and after, and, as I said, they both contain my data. I would attach them here, but I won't for obvious reasons. (And it does not easily reproduce since the db needs to be large enough.)
I also checked the other files and it seems they all get cleared correctly. I might try this on some other systems some time, but if someone else could confirm that it's just cookies or that it sometimes happens to other databases too, that would be great.
I know that VACUUM is pretty slow, but considering that the database is empty, it shouldn't be too bad (unless it's Places). I also know that after a VACUUM, the data still remains on the hard drive, but I'm not really concerned about it since it's not as easy to recover it as opening a file with Notepad.