QR codes not uploading to ODK

We are collecting samples in the field, and labeling them using sticky labels with QR codes associated to a number, which we scan after entering the rest of the information for that sample.

The ODK form includes other info such as dates and site of collection. However, when I went to download the .csv file, I found that none of the QR codes had uploaded on to ODK, it's basically an empty column. For some reason only the last two uploaded, of around 4,000 entries! The rest of the information uploaded fine. The codes are still in the phones we used to input the data (and we used 3 different phones to do this), but I am worried that if something happens to the phones we will lose all this information.

Is there a way to extract this information from the phones?

Any guidance is much appreciated!

What server are you using to host the data? ODK Central? ODK Aggregate? Something else? If you don't know, providing a link to the server would be sufficient.

My guess is that you are using Central and that you updated the form at some point and renamed the QR code question or put it in a group. Is that correct?