@catcat it really is difficult to understand waht is happening. Things to consider.
How large is the data in its initial (compressed?) format. If the file might contain a lot of missings a CSV file might be shrunk to impressive (small) numbers.
Do you see the data within KNIME and are the number of lines the same as in the initial CSV. You can export data from within KNIME at every step of the way and check if you still have the right amout of data.
You might want to create an example with artificial data where your problem can be demonstrated. Yes that is some work but it will make it much easier to get help in the forum.