Hey Thomas,
If you see the "First update" section of the step-by-step walkthrough we tell you to include all the files from every version of your app. wyBuild takes care of comparing the differences between the versions, generating patches, and creating a list of files and folders to remove.
If you only include some of the files of updates then you'll run into problems that you've been seeing.
As i saw the updater gets only the files from the latest version bypassing all the others (1.0.1, 1.0.2, 1.0.3, 1.0.4) as result to miss upgraded files. Is that correct?
wyBuild doesn't do incremental patching (e.g. 1.0 -> 1.1 -> 1.2 -> 1.3) but rather creates updates from "oldversion" to "newversion" (e.g. 1.0 -> 1.3, 1.1 -> 1.3, 1.2 -> 1.3). Then wyUpdate chooses the correct update file to download based on the version of the app they have installed.
Tell me if this helps.