Hey William,
Multi-select treeviews are exceedingly hard to do right. We started an effort to make this a couple of years ago and it balooned in size, scope, and difficulty really quickly.
Now, to address your question more directly, why are you deleting files from your versions? Why aren't your clicking the "New version" tab and dragging your latest files? wyBuild takes care of making the smallest patches for you by comparing your old files with your new files.