Downloading large amounts of data, csv Urgent!

We have a form with an initial question and then a repeating group attached to it.
The data collected so far has over 380,000 rows of data, with 10 or more rows of data in the repeating group. This means we have over 3 million rows of data there.
If we select XLS as a download option we get two tabs, the first with the 380k rows of data and the second tab cuts off at the limit of Excel (just over 1 million rows).
If we select CSV we always get the 380,000 rows.

Q. How do we download the full 3 million rows, (preferably in CSV as I don’t think you support multiple excel files?).
Perhaps it is possible to filter the dataset we download (so we can use XLS) or possible to access the second datatable in CSV?

Background: We are a charity whose partner organisation is using KoboCollect and storing the data via the KoboToolbox. We are currently undertaking a mass distribution of aid in the country and need urgent access to the data in order to monitor progress. Our partner has tried to get around the problem outlined above by using ODKBriefcase which has been working, but is now throwing an error when pulling the data. We have stepped in to help here and are urgently trying to find ways to allow them to obtain the data.

Many thanks in advance for any assistance.