If you do:
SELECT U_Username, U_Groups FROM 'w3t_Users'
WHERE U_Groups NOT LIKE "%-3-%"
ORDER BY U_Groups
If the U_Groups values you want to change are all the same, or there is only a few variations:
UPDATE 'w3t_Users'
SET U_Groups = "NEWGROUPVALUES"
WHERE U_Groups = "OLDGROUPVALUESTOREPLACE"
Something like this for example if most of the users are only "-6-":
UPDATE 'w3t_Users'
SET U_Groups = "-3-6-"
WHERE U_Groups = "-6-"
Or do I not follow what you want to do?