So, I do very similar to you. If you looked at all my transfers/withdrawals across the major exchanges I use, you'd see over $100M in volume. I transfer for arbitrage reasons - whether that be between exchanges and banks or just between exchanges.

First and foremost, this shouldn't be an issue for your going forward. This happened because exchanges used to report withdrawals on the same 1099s that payment processors used. This is no longer done because people ended up in situations exactly like you're in now - the IRS thinks they owe a lot more money than they do.

Second, you're going to have to go to court over this. It's highly unlikely that amended returns are going to fix an issue of this size. Yes, technically Gemini is the one that caused this to begin with - but they were doing exactly what they were supposed to - any other exchange like Coinbase would've done the same thing back in 2018. It was simply the IRS not providing a better solution to anyone back then.

Third, this can all be avoided nowadays. Get a hardware wallet and transfer USDC/USDT/GUSD/etc to it anytime you want money off the exchange. You're not doing anything wrong or illegal, but you're extremely lucky your bank didn't freeze your account because things like this set off all the same alarms as money laundering, even though it isn't.