@lauresp The data isn't lost, it's just hidden. If you delete a field (typically by renaming or by adding/removing it from a group), Central hides that deleted field in export. In the next release of Central, we'll warn you about this behavior and we'll also let you export this missing data as well.
For now, you can add the missing questions back to your form, but set relevant as false(). This allows the data to show up in the export, but those questions are hidden to data collectors. You can learn more about this technique at Can you still send data from old versions of forms to ODK central - #5 by LN.