If you took less out of the Roth IRA because of the loss but put funds in the Roth IRA via conversion and therefore, the value is not $0 on December 31, 2024, then the 6% penalty will be calculated on Form 5329 for 2024.
For example, if you made an 2022 excess contribution of $7,500 but only removed $7,000 in 2024 because that was all that was left in the Roth IRA account, then you still have a $500 excess contribution left. If your balance is $0 on December 31, 2024, then the penalty will be $0 because the 6% penalty for 2024 is calculated as the smaller of the excess contribution or the value of your Roth IRAs on December 31, 2024 (including 2024 contributions made in 2025). And the excess contribution will resolve because of the Form 5329 line 18 instructions. But if you add funds with the conversion and you balance at the end of 2024 is now $7,000 then the penalty will be $30 ($500 x 6%). And if you don't remove the excess contribution in 2025 then you will have to pay the 6% penalty again in 2025.
I would recommend to wait to convert you funds in the traditional IRA to Roth IRA until 2025. You can track the nondeductible traditional IRA contribution on 2023 Form 8606 line 14 and can enter this on your 2025 return when you make the conversion.
Your 2023 6% penalty will be calculated on Form 5329 part IV and will be the smaller of the excess Roth IRA contribution $7,500 or the the value of your Roth IRAs on December 31, 2023 (including 2023 contributions made in 2024).
@AprilWang
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