you could setup a separated backup mount location for these and then making that non browsable, I think that should then stop them showing. Can just enable the browsable option if you need these to show for whatever reason
In the QMC, system > setup > folders is where you can manage your mounts.
I would probably set up a new task prior to your application reload, which is solely a distribution job to the back up mount location you create.
That is assuming you have publisher though.
If you need to do it without publisher, you can probably just create a back task qvw executing the required command lines to copy your application to your backup folder (and make that task run prior to main reload)