phpMyAdmin does not write any database files. It is a php client application which accesses a MySQL server.
On OSX the MySQL server creates its data files in /usr/local/mysql/data as far as I know.
1. Stop your MySQL server
sudo /usr/local/bin/mysql.server stop
2. Remove new data files
sudo mv /usr/local/mysql/data /usr/local/mysql/data.new
3. Copy old data files from your backup and fix prrmissions
sudo chown -R _mysql:wheel /usr/local/mysql/data
4. Start your server again
sudo /usr/local/bin/mysql.server start
5. Check and optimize databases
sudo /usr/local/mysql/bin/mysqlcheck --all-databases
Now phpMyAdmin will show all old databases