I would not change the numbers downloaded from the brokerages! If you do that, attach an explanation to your return. If the IRS computer kicks you out because of the different total proceeds amount, it will end up on somebody's desk and the attachment will be enough to not receive a letter from the IRS. That is much less work and will be much less frustrating than having to answer letters from the IRS.
The best solution is to wait a little bit longer: I'm sure that Intuit will revise its position and ultimately agree with Fidelity, Vanguard, TD Ameritrade, and the IRS that negative proceeds are allowed in Box 1d (Especially, if more people call their brokerage and complain that their reported numbers are not accepted by TurboTax: These brokerages have more cloud with Intuit than we have).
If you owe money, and can't wait to pay, ignore the error messages about the negative amounts and print the return. The printed return is as it should be and you file it as a paper copy. If you get a refund, do this only if you can wait for your refund for a long time.
The last option is to change platforms.
