wyBuild creates "direct patches". So if a user has 1.0 installed and you've since released 1.0.1 and 1.0.2, then the user will download the patch that goes from 1.0 to 1.0.2. It doesn't touch the patch for 1.0.1.
So should you delete "intermediate" versions in wyBuild? No. Here's why: any user on a version that you delete will be "stranded" on that version. That is, they won't be able to update to the latest version of your app.