It sounds like somehow after whatever happened in 2016, she was signed up for an IP PIN.
Phone the IRS special office that handles IP PIN issues. Tell them what is happening and the problem you are having establishing an IRS account. I don't know if it's possible for her to establish one yet or not.
When you phoned the IRS, is this the number you used? You may have phoned their main number. The one below is the special number shown on the IRS page about the IP PIN. They should be able to answer any questions about an IP PIN. This special office is usually easy to reach.
https://www.irs.gov/identity-theft-fraud-scams/retrieve-your-ip-pin
800-908-4490 for specialized assistance, Monday - Friday, 7 a.m. - 7
p.m. your local time (Alaska & Hawaii follow Pacific Time).
If you can't get the IP PIN online, they can mail one, but it may take up to 21 days according to that page. Plus, since she has never filed a return, the verification process when speaking to someone on the phone might be more complicated. So you'll just have to see what you find out when you speak to someone.
So depending on what they tell you, you'll have to decide at some point whether you will be able to efile or whether you will need to print, sign, and file by mail.
If you are SURE you are due a Federal refund, there is no penalty for a late Federal return. State rules might vary.
If you owe taxes due, however, and did not file for an extension, then you should file and pay as soon as possible since penalties and interest are accruing.
