You need to follow the step-by-step walkthrough: http://wyday.com/wybuild/help/walkthrough.php
Specifically you need to follow step 6. Where it says to add all files in wyBuild. Why? Because wyBuild compares your versions and decides the best thing to do to generate the smallest possible patches. If you don't add all files then wyBuild will mark files that are present in an "old" version but not in a new version as files that need to be deleted.
Make sense?