wyUpdate only rolls back updates if there's a failure in the update process (a file fails to get patched, it can't get access to a file, etc., etc., etc.).
Outside of the update process (i.e. after an update has successfully installed) then the rollbacks are up to you. So if you made a mistake in 1.0.0.2 and you want to rollback then the way to do it is to create a version 1.0.0.3 (or 1.0.0.2.1) in your wyBuild project that contains the 1.0.0.1 files.
In other words, pick a new version in wyBuild greater than the previously installed version.