After reading your file, I'm not sure what can be done to undo what's already been done.  I think a better solution would have been to reduce the assessments for everyone for the upcoming year(s) until the excess has been used up.  Maybe the way to correct it is to reduce upcoming assessments of those who should have received the refund and didn't, and calculate how much is owed back by those who received a refund who shouldn't have, and keep their assessment where it was until they have paid back the difference.  But the math could be kind of complicated, and I don't know what your bylaws allow when it comes to re-calculating assessments.

In light of that information, I will repeat my first suggestion - " I think a better solution would have been to reduce the assessments for everyone for the upcoming year(s) until the excess has been used up. "  

As for how to correct what's already been done, that's a challenge.  You could let everyone know the refund was contrary to the laws for Non-profits, and ask that they pay it back, but my guess is you'll be fighting an uphill battle.  If the amount is significant, you could try taking them to Small Claims Court, which can be done without an attorney.  (Attorney fees could quickly eat up the funds you're trying to recover.)  I'm not sure what other enforcement powers you could call on.  Maybe ask the Attorney General's Consumer Complaint department?  I don't know if they would handle that sort of thing or not, but it wouldn't hurt to ask.