On the application side the effects were quite bad, as the data was mainly XML and, depending on where the bit was flipped, it could impact the data or the XML structure. The data had its own CRC/hash, so the packets were cleanly rejected by the application. Unfortunately the XML library from the message queue engine and the ESB we were using did not like at all when the bit flipping occurred in the XML tags (it seems fuzzing tests were not done at that point) so the message processing got stuck and we kept getting bad messages in the queues. Even worse, the queues could not be cleaned with the normal procedures because the application wanted to first display info about the messages inside - and that failed.
The network debug was non-trivial because of that header consistency - the network devices did not report any kind of packet issues, so we had to sniff the different network segments to identify the culprit. From the application point of view, we had to delete the whole message queue storage to get rid of the bad messages, and let the application handle the rest (luckily it was designed with eventual consistency and self-healing).