Should departments have a policy regarding updating online resources?
Fundamentally, I don't think this problem has to do with the shift to a paperless format. Even with a syllabus on paper, my experience has been that a professor may well change it, often for good reason (e.g., shifting to make room for an excellent guest speaker, extending a deadline on a lab that many people are having problems with).  

I think that the real problem here is that the faculty member has made a last-minute change that makes life harder for the students.  Student who thought they were done with the assignment have just discovered that they have more work to do, it may be interfering with their other plans, class or non-class, and it just plain doesn't feel fair.  Perhaps a good policy for that would be that no assignment can be made more restrictive once it has "started"?

There is also a place where the electronic aspect can enflame or mitigate the issue, and that may also address your original question.  Online documents offer the potential for making a "sneaky" change that is not announced directly to the students.  That seems to me to be something that should definitely be prohibited, and might be handled automatically by having the system send an announcement to all of the students whenever a course document changes.  I don't know Moodle, so I don't know how hard or easy it would be to set up automatic notification; even without automation, however, you could certainly regulate that all non-trivial changes must have a notification sent to students.