Prevent from erroring on unrecognized submodules

The current method of submodule handling can put the repo into a bad state if the mirror for a repo isn't listed as an alias of that repo, since subsequent synchronize_submodules calls won't be able to get settings for the new URL.
To prevent this, we can accept URLs for any repo that we don't have information to rewrite, since the update could still pass if the URLs are already rewritten.