I see. This could be due to the following:
You have a survey form on the server and you download the same as a blank form in your Collect app. You collect your data in the app. At the same time, you delete (accidentally or on purpose) your survey form from the server. The blank form and the collections that are in your Collect app do not get synced to the server.
So the first check you will need to make is to see if the survey form exists on the server? Please note that it should be the same form that was pulled to the Collect android app. It cannot be a different form like say, you first uploaded a pilot form to test the questionnaire. Then collected the submissions for the form. At the same time, you deleted the project due to some reasons from the server and you upload the same XLSForm. This too should not work. The submissions to be synced with the server require the same survey form that was uploaded at the beginning.
Maybe you could test what I just outlined with a dummy project to get a better understanding.
