Data edits lost after data cleaning

In July we made changes in the data submissions including deletion of some submission which were successfully saved. In September, we went back to check on the data submitted and found out that all changes made in the submitted data have been lost (replaced with the old data). We are using the humanitarian aid server. Our data is mostly submitted via KoBoCollect. The editing is done via the web-interface.
What could be the issue?

Welcome to the community, @hassenmeier! Was this project your own project or was it shared to you by someone else?

It was a project I worked on. I am a consultant in the process, providing backstopping support. And, now I have no clue what happened. One option we see is that the enumerators’ devices will have the data stored on their devices and overwrite the changes. But I could not figure out how this could happen.