Unlike what Srik wrote - you shouldn't carelessly delete the old .wlapp. By doing so, users who use the version of said .wlapp will not longer be able to connect to the server.
So you if need to trigger a direct update, re-deploy the updated .wlapp file when you need to, don't first delete it.
Do not delete it even if deploying a new version (1.1 instead of 1.0).
You should delete only after you are certain that all of the users of 1.0 have migrated to 1.1.
1.1 constitutes of a new version that was also uploaded to the app store.
You can force users to upgrade by "remote disable"ing v1.0 (and point to download the new version). When everyone migrated, you can then delete the old version if you really feel like it.
Deletion is done via MobileFirst Console.
- Load the console URL
- Click on Applications
You can delete:
- The entire all with all of its environments:

- or a specific environment, or a specific version of an environment (if you had for example 1.0 and 1.1):
