Grade changes with auto grader
If any student feels disadvantaged by this, then you will have an uproar and complaints to administration. You describe a system in which they depended on the actual thing you built not some "instruction" you gave. 

I would guess that you are stuck with the thing for this group of students, both practically and ethically. Otherwise grading will seem chaotic and unfair to them. Your reputation might suffer both with them and with your boss. 

This sounds more to me like a case of releasing untested or insufficiently tested software. 

One way out would be to void the results of the autogravder for anyone disadvantaged and give them one additional attempt to submit. But that could also be a problem because of time constraints on other things in your course and in their other courses. 

Live and learn. But first, be fair.