Apologies for not replying sooner. After a few days, we actually found out the cause was a user turning off all triggers on the table, forcing some data into it to try and solve an RMA issue manually, then turning the triggers back on. This hadn't showed up on any logs, and after finding zero signs of corruption or other FKs being violated, we asked the for more information about what had been done recently and they fessed up.
So, relief on one hand that there was no data corruption. But a bit troubling that the user did that :p