I think that by "remove" you mean select the lines with indexs and DROP them and recreate?
I'd add that these may not drop -
The column name 'group' is a MySQL reserved keyword.
The column name 'key' is a MySQL reserved keyword.
When I backed up the database and did a drop on all, I got this message -
#1090 - You can't delete all columns with ALTER TABLE; use DROP TABLE instead
ALTER TABLE `ac_settings` DROP `setting_id` ,
DROP `store_id` ,
DROP `group` ,
DROP `key` ,
DROP `value` ,
DROP `date_modified` ,
DROP `date_added` ;
I deleted group and key individually, and re added. They listed as Primary Keys so nothing changed. The 1.2.7 update.sql file will not import so I'm back to where I began.