What happens when you try to resend? Does Collect show any kind of warning or error? Does it show that the submission was successful? If it is showing that the submission was successful, then it's likely that Central does have it already. How are you determining that it's not in Central? Could something in your processing and analysis pipeline be missing it instead?
What probably happened is that the user initiated a send and/or autosend ran and at that same time they made an edit. This is one of the many reasons that we've made finalization truly final in the latest Collect version.
If you want to be absolutely sure that you're not losing something, you could pull the instance from the device using adb or view it using a text editor to compare with what's on Central. Maybe the user did make a legitimate edit that you'd want to apply on Central.
I resent the whole form after I renamed the instance file and directory and I got all the data in central. 3 were duplicated and I deleted it from our final database.