Looking at how banks handled these kind of issues in the past, they'll shut down all operations for these few seconds and throw away anything that still came in these seconds as invalid.
It sucks for their customers and partners, but that would be a decent conservative option I think.
Somebody should have told the financial institutions in Batman: The Dark Knight Rises that throwing away very obvious unwanted transactions was an option!
It sucks for their customers and partners, but that would be a decent conservative option I think.