Owner has over-payed HOA assessments for years

We have an owner who has been overpaying his assessment for 16 years. There was an unofficial change to the CC&R stating everyone would pay the same fee regardless of ownership since the difference was/is negligible for all units but the only 1 bedroom. My question, do we owe the 1 bedroom unit for all back assessments? Is the unofficial amendment (not filled with the clerk), voted on by the board long ago valid? Is there a statute of limitations for back assessment? He hasn't paid in 9 months and this issue needs to be resolved.