When a multi-billion dollar transaction occurs between two companies, how are the funds transferred/managed?

Typically by Wire Transfer.  Wire Transfers, unlike checks or regular electronic bank payments (known as ACH transactions in the US), are irrevocable once final -- even in the case of fraud. (That is, if someone authorized to make a wire transfer makes one, even if defrauded or illegally embezzling funds, the accountholder are still liable for the payment. If someone at the bank who isn't authorized to make a wire transfer illegally makes one, the accountholder is not liable.)

The idea is that businesses need finality when they receive payments, they can't just have money disappear from their accounts like if a "chargeback" or "stop payment" is done. If a wire transfer is made and you need your money back, you have to sue the recipient -- you can't just ask the bank to reverse the charge. For transactions between businesses, it's assumed that the need for finality outweighs the fraud protections that checks and nonwire electronic payments provide. (In the US, wire transfers are rarely used by consumers. Also why scamsters try to get you to wire money to them - people wrongly assume that wire transfers have the same protections as consumer payment systems.)

Source: The Uniform Commercial Code Article 4A.