That the distribution reported on this code 1 Form 1099-R can be treated as a Coronavirus-related Distribution means that you can get the money back into your SEP-IRA and, if done before you file your 2020 tax return, will not be taxable on your 2020 tax return. That would still leave you with the excess SEP contribution to resolve.
You shouldn't have to amend your filed 2019 tax return since only the deductible (non-excess) portion of your SEP contribution would have been reported on Schedule 1 line 15. Even if your 2020 net earnings were less then in 2019, you would only need enough net earnings to be able to absorb the excess, not the portion of the contribution that was deductible on the 2019 tax return. If net earnings in 2020 were not sufficient to allow all what would have been an excess contribution for 2019 as be allocated as a 2020 SEP-IRA contribution, you should be able to obtain a return of that excess contribution for 2020.
For example, lets say that you were eligible to make a SEP contribution for 2019 of $20,000 but mistakenly contributed $30,000 in 2020 that was originally intended to be a contribution for 2019. Because the contribution was made in 2020, you can treat that deposit as being a combination of a contribution of $20,000 for 2019 and a contribution of $10,000 for 2020 (which you would need to document in your company records). Then, if your 2020 net earnings will only support a $6,000 SEP contribution for 2020, that would leave you with a $4,000 excess contribution for 2020 that you should be able to have returned by an explicit return of contribution (not a regular distribution) before the due date of your 2020 tax return, avoiding any need to file any Forms 5330 and pay any penalties.
