As mentioned, you could bypass it just to get your site back online. The problem with doing this, is you dont know if your server is seeing an old version of the file, or if permissions are incorrect what other implications it will have for the upgrade. And of course you will have the same problem on the next upgrade as you havent really solved the issue.
If you do decide to do this, please ensure you remove the line afterwards, as leaving it there will never check anything. Which could cause you a lot more issues.