Hey Carl,
No, wyUpdate doesn't currently check file integrity of the files. I should restate that: wyUpdate doesn't check file integrity of the files that won't be patched. If a file is to be patched as part of the update, and the patch fails to apply, wyUpdate downloads the "catch all" update (which consists of the full files) and just overwrites any user-modified files.
If a user modifies a file, and the file isn't patched as part of the update, wyUpdate just ignores it. It doesn't look at it to see if it's valid.
That being said, we're thinking about adding this. Probably around the time we add the feature to do "web-installs".