Thank you for your question and patience, I’m Tom and I’ll try to help you.
She will be fine. Her right to stay in the UK is highly unlikely to be in jeopardy. It is not mandatory that she must have anything other than her passport.
Because she has worked in the UK for longer than 5 years, she would be regarded as having “permanent residence”. However, because she has not (I presume) yet applied for confirmation of her PR you do not actually have a document which formally states that she has it. Having a PR card is not a requirement, but it can be helpful.
So, I would suggest that she applies for PR (https://www.gov.uk/apply-for-a-uk-residence-card/permanent-residence-card ). Once she has this, it is proof of her right to remain in the UK without making any further immigration applications.
One small note of caution is that it takes around 6 months to be given the permanent residence card after she applies and she would be without her passport for the whole duration of the time they are deciding the application so she would have to reconcile herself with not travelling outside the UK during this period of time.
My goal is to provide you with a good service. If you feel you have received anything less, please reply back as I am happy to address follow-up issues specifically relating to your question.