The database was in latin1 sweedish colation and this had some side effects with the Greek characters.
FIRST THING: GO TO PHPMYADMIN AND EXPORT DATABASE TO HAVE A BACKUP!
Then I went to administration, utilities, database status, download backup.
This makes a good backup with proper encoding inside. (for me this was the right version and not the one created with phpmyadmin)
I opened the .sql file with Notepad++ and I replaced latin1 with utf8 in all the document. Save.
Then I went to phpmyadmin and i checked all tables and then selected the action drop. I confirmed dropping the tables, and then I went to import.
I imported the new sql file I created with Notepad and then I checked the database structure, tables structure and browsed some of the data. Everything appeared perfect!
Loaded a sample page of WHCS but all the Greek characters were corrupted and looked like ?????. After some research I added this line in configuration.php
Now everything worked perfect! I checked the database again and I made sure that the database collation was utf8_general_ci (if it isn’t go to operations and change collation).
I’m a happy Greek user of WHMCS now!