Can I file an amended return and a NY return for my daughter who filed a Federal return on an other site?

Yes, you can do this in CD/download program you have.

What you have to do however is first enter the return exactly as she filed it.  You would then show it a filed by mail (regardless of how it was filed).

Then you would come back in the program and Amend the return.

Which will need to be printed, signed, dated and mailed to IRS and NY.

https://ttlc.intuit.com/replies/7276601