Yes, let's say you have version 1.0 and version 1.1. Let's say you have a shortcut named "Old" on your desktop in version 1.0 and you want to change it to "New". In wyBuild, after you've added all your files (see the step-by-step walkthrough) create a shortcut for your file in your 1.0 version (by right clicking, then clicking Create Shortcut). Rename it to "Old" and drag it to the "Common Desktop" folder. Do the same in the version 1.1 tab in wyBuild except this time name the shortcut "New".
Now when wyUpdate installs your updates it will delete the old shortcut and install the new one.