There is no logical explanation for your loss of questions based on information so far. Just curious…
Did you ever back up your survey to XLS as you were working on it? I am assuming that the answer is no. However, if you did, you could potentially go back and see where the questions started to disappear, and you could possibly restore your work.
Did you view the form frequently as you were building it? If so did it function correctly up until this last attempt to save and deploy?
Did you successfully deploy the form as you were working on it? Did it function correctly? I have been copying and pasting the URL into another browser, and so far both Safari and Opera have worked ok. (Although Chrome will be the preferred browser.)
If so, did you download the data after testing the form? This would be additional proof that your work-in-progess was functioning normally.
If you did not view, deploy, and view data as you were building the form, it seems that something else is going on. For example, are you building on the same server at all times.? There are 2 - humanitarian response and personal.
If there is no explanation, and no backups, then it seems that you have no alternative other than to rebuild this entirely. Let me suggest the following, and you may be doing this already.
As you build, view and test the form functionality frequently. I usually view after adding each question, but at least after adding several questions. Save each time. It only takes a few seconds.
At least once a day, save and deploy your project. Test it in another browser or KoBoCollect. If it looks good, download your test data and review it quickly. Finally, download your current work to XLS as a backup.
If you figure out where the error occurred, please let us know for future reference.