Files and Folders Deleting

My apologies if this has been asked before but I think this is more of me not exactly understanding how the whole update process works. I did a quick search but didn't exactly see what I'm looking for.

I have pushed out an update and now need to push out another. The software has some supporting files in a couple of different folders under the C Drive. If the user puts any files/folders in those folders will those files/folders be ignored or deleted? If deleted, is there any way to tell the updater to ignore any files/folders it doesn't know about in those folders?