Answer by Mendix Support:
By design the Create Backup operation creates a single transaction when backup is started, any changes after this “point” will not be "visible" to the task. So to answer the question:
Lets say the backup takes about 30 minutes. We start the backup 17.00 and stop the app 17.25 (just before the backup finishes), when the backup is finished, we deploy and start the app. In the meantime (between 17.00 and 17.25) changes in the database can (and will) occur. Will changes made between 17.00 and 17.25 be included in the backup?
No. changes between 17:00 and 17:25 will not be included in the backup.