This is not a general problem with ManifoldCF, because we even have tests that exercise this functionality. Probably the issue is that some JDBC drivers are more resilient than others. I have not researched what the MySQL driver does in this case, but I wouldn't be surprised if the pooled JDBC connections for MySQL were not resurrectable after that sequence of activity.
If there is a general JDBC method we could call to verify that the connection is alive or dead, it would be easy to discard the dead ones and recreate them. But this indicates that no such general functionality yet exists: