I would. I dont think they get scheduled again with an amended return, but better safe then sorry.

Okay.

If on the e-filed amended 2020 with boxes unchecked the payment is not withdrawn , then the payment can be made online.

Thank you.

Thats the plan I would use. Im honestly not sure if the amended return efiling would pick up those scheduled ES payments or not, I think a better plan would be to make them at IRS Direct Pay wesbite.