Yes, publisher creates distribution copies of the files. To remove them from Access Point, I believe you need to delete the distributed files. Where they are stored is a matter of your Publisher configuration. In 8.5 at least, you can check the distribution task to see which resource is being used. Then you can go into Resource Management, pull up the resource, and see where the files are actually going. In my case, I got an access denied actually getting to the specified server directory (something I need to fix since on paper at least, I'm one of the QlikView Publisher administrators), so I can't verify for certain that I'm on the right track, but I believe that's how it all works.
Maybe we'll be lucky and someone with more of a clue will chime in.
I had the exact same problem. John is correct. In my particular situation, we were publishing apps to a web server. I had to actually go into the web server, where our access point was pointed, and remove all of the documents related to the older version. I believe there were 3 documents that our publisher created (and *.xml, *.qvw, and a shared documentment in some instances). I had to remove all three in order to elimiate them from the Access Point. Hope that helps.
In your Publisher/Control Panel, down the left side under Main click Resource Management. Now in the right hand pane under Other Resources click your Access Point Resource this will show you the path to which you are posting your AccessPoint docs. Alternatively you can go into your QVS Management console and this path will also either be your root path or a mounted folder. I usually set these up with a service account that has full NTFS access to the path. Then just use that account when editing or removing files.
You can also create a job in publisher to run a .bat on a schedule to go to this folder and remove files that are out of date. Something like the forfiles command explained here http://www.dialogmedical.com/kb/000026/DeletingFilesByAge.pdf .