Hi @Topsy1980 and firstly I am sorry that your DD has struggled so much. I hope that she is doing better now.
Speaking as a former secondary teacher, I think that a student who had missed such a lot of KS3 would have a real challenge catching up to the level of others. In linear subjects like maths, some science, MFL and Eng lang, as others say, she could be a long way behind. Less so in topic-based subjects like history and Eng lit.
You say you asked for schoolwork though I can also see why this was difficult for the school with such long absences; did she do any other structured work? For example, did she work through the KS3 guides for various core subjects such as science, English, MFL? If so, can you evidence this to school?
Also it’s not clear what the higher and lower streams are? At my DCs’ school, students were (kind of) streamed for science – as in, more able students were in triple, others too double (in more or less the same time). So I guess there was a similar situation. But it might be much better for her to be in the groups where the pace is easier. Foundation science and maths would give her a good basis to move on post-16. Can you reframe it to her in that way perhaps – as a positive move?
How does she feel about going back to school overall? Might online school be a better option?