I need to break this down a little...

"It was mistakenly treated as a SEP contribution on 2021 1040 which was also not deductible.)"

Which means it is not also a nondeductible Traditional IRA contribution, as you put in the title. It isn't both. And that is associated to a business return, so are you sure it isn't (for instance) part of the Sched C info? Specifically, which account Type did this get put into, and how it is listed on the 1040?

"The $6,500 excess was NOT withdrawn before 12/31/22"

If it is for tax year 2021, you have until the tax filing due date of the return plus the time of extension to be considered timely filed (Oct 2022). However, that goes back to the employer, which typically means amending the return. Now that would include amending 2021.

"and is still in the traditional IRA account as of 3/10/2023."

Then the error carries over for 2022, as well.

"1. Should the 2021 1040 be amended to show the excess $6,500 on form 5329 and $390 additional tax due, i.e., 6% penalty on excess? (10% penalty not applicable as client is over 59 1/2.)"

The over 59 1/2 would apply at the time of distribution. But that doesn't go back to the employee. You'll have to do some research.

"2. If #1 is the correct approach, and contribution is not deductible on 2022 1040, can it be withdrawn before April 15, 2023 and avoid the 6% penalty for 2022?"

I think you are trying to apply some sort of carry over rule? "Excess contributions left in the employee's SEP-IRA after that time will be subject to the 6% tax on the employees' IRAs, and the employer may be subject to a 10% excise tax on the excess nondeductible contributions."

https://www.irs.gov/retirement-plans/retirement-plans-faqs-regarding-seps

"4. By what date should it be withdrawn to avoid further penalties?"

ASAP. That stops the bleeding.

I've not run into this for SEP, so am not much help; you need to do the research. This reply assumes you are working for "taxpayer as employer/employee."