That mod forces user to change his e-mail, but he will receive e-mails still. The only way is:
That app is helpfull of course, but not a solution to stop sending mails to selected member.
First question - do you want to keep your 4.1 customizations? It yes then the answer is - hold with the upgrade and work with a upgrade but of these customizations first!
You can open PhpMyAdmin (if you have access), find any corrupted tables, check them and use Fix option from the dropdown.
More info - https://www.nexcess.net/help/how-to-repair-mysql-tables/