I'm not sure if I precisely understand the problem, but have experienced similar issues (I think!) when using mysql encode() and decode(). You can easily change collation:
alter database [dbname] character set latin1, collate latin1;
This can also be done table by table.
Specifying Character Sets and Collations [dev.mysql.com]
Database Collation [dev.mysql.com]
Table Collation [dev.mysql.com]
Another problem I often encounter when changing versions, "Client does not support authentication protocol" when trying to connect with the same password. The encryption methods changed from one version to the next.
SET PASSWORD FOR 'some_user'@'some_host' = OLD_PASSWORD('newpwd');
Hope this was on the right track . . .