say that it is done intentionally but could not point anyone because
we did not enable the logging feature in MySQL.
You already said it yourself: you don't have logging enabled, so that data
is not available.
If you have binary logs, you could comb through those for the delete
statements; that'll at least give you a timeframe.
I would also go through the logs of whatever other entry vectors exist to
your database (apache, for example) for suspect looking statements or
logins. Also I'd check the history files such as .mysql_history and "last"
on the database server to look for anything suspicious.
Is it possible there is filesystem corruption which is actually responsible?
Take the server offline and run standard diagnostics such as fsck, perhaps.
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