Left Employer on March 31. They mistakenly ran an extra payroll for April. They request I pay net amt back? Net amt >10K. Taxes,401k deducted. How to handle at tax time?

ask your ex-employer about how the 401k will be handled. As for other items since the paycheck and repayment were in the same year the IRS dictates that your W-2 should only reflect the correct (net) amounts.  example if including the April paycheck your federal withholding was $6500 and that April paycheck which you repaid showed $1000 in federal withholding your 2024 w-2 should show only $5500 in federal withholding.  So there really is nothing extra you have to do when doing your 2024 return. 

Since everything happened in 2024, your W-2 should reflect reality (after adjustments), and you should not need to do anything special on your tax return.