Glad your data is ok, as far as i understand it, the collation only affects sorting, and the benefits for
utf8_general_ci is it's better at sorting non-ascii characters, especially capitalised ones, so a probable fix (after taking a restorable backup ;) would be to change the collation on the
utf8_general_ci tables and fields to
Which version of MySQL are you on? Maybe a minor update made it more sensitive to this?