You free app does have a different database then your local application. So changes in the local database, will not affect changes in the free clou database.
It is also very recommend to not delete user (or any other data) directly in the database. You can better build this functionality yourself in the Mendix application. This way you know for sure you are deleting the right data. For deleting the account, there already is some default functionality in the administration module.
If you deploy to a cloude node, you only deploy your system logic, not your data. If you want to delete users on the cloud, you need to to this on the cloud. What happens in the cloud stays in the cloud and what happens on your local machine stays on your local machine (As long as you don’t upload a dump of your local database to the cloud and restore it).