Hi Todd,
That's a fair question and one that MyOpenMath would also need to be asked I think. We can easily change the tool version over to 1.3 from 1.1 (as I'm sure you've seen. It can even be done via dynamic registration), however what the tool does with an entirely different story. There is, in one of the migration specs, a migration claim that can be included to migrate a tool from 1.1 to 1.3 during a launch, but we won't send that (not supported), so the tool won't know that a given consumer key maps to a registration/deployment and may end up creating an entirely new one.
Some of the considerations for this, in general:
1. Do existing users who have launched into the 1.1 tool need to continue to have access in the coming semester for any reason (e.g. to view the activity or see results breakdowns etc)?
2. How will the tool handle a 1.3 launch WITHOUT a migration claim (e.g. will it create all new users etc)?
If the tool can't identify the original 1.1 tool and a user launches into the tool from a 1.3 tool (the updated tool), there's every chance that the tool will be unable to show them what they'd previously done - and that's the main concern here.