the data from the last 50 questions are missed
Are the visible in Collected Data -> View Dataset? Is there data in these cells?
How many variables do you have? Possibly, you just exceed the limits of Excel. You can open the CSV file in Notepad++ and simply check in the raw text if the variables are included in the CSV file. This will allow the distinction, if it's an export or an import problem.
You may give LibreOffice Calc a try. This is more potent than Excel in many ways.