This shouldn't happen, in fact we have a number of algorithms in place to prevent this from happening. That is, wyUpdate explicitly verifies a file's integrity when the file is extracted from an update. And if the file is a patch, the integrity is checked again after the destination file is patched. If at any point a file becomes corrupted as a result of either the extraction or patching process, wyUpdate rolls the update back to the last good state.
In your wyBuild project make sure the file referenced in the new version tab references a fully valid file (and not a 0 byte file). Also, can you reproduce this behavior? Try rerunning the update, do you get the same result? Send me all relevant files (the updates, the wyBuild project file, the source files) to wyatt@wyday.com.