Fix patch_upstream script on Windows

Preventing failure while applying patches on submodules that are
skipped on Windows.
Non Windows related submodules are not checked out from upstream
repository. This behavior is a workaround for git issues.

Change-Id: If34d9d2916829f87c7397a07803f79c156c05c57
Reviewed-by: Michael Bruning <michael.bruning@digia.com>
Reviewed-by: Andras Becsi <andras.becsi@digia.com>