The auto debits have already been scheduled and this will not change them. Just to be sure remove the check marks to do auto debit. Override the estimates to be the specific numbers of the original return. 

Even though the PFL is not taxable to CA, you should probably amend the CA to have the new Schedule CA match up to what they will get from IRS once amended. 

I do not believe you can pay the 1040x via auto debit. If not give the client instructions on how to pay online with https://www.irs.gov/payments/direct-pay