It's very easy
Go into the View All General Settings page, hover your mouse over the group to remove, and look for this part of the URL:
QUOTE
...&code=setting_view&conf_group=XX
The number there in the red is our critical piece of data. Use that to run the following queries in your SQL Toolbox:
SQL
DELETE FROM ibf_conf_settings WHERE conf_group = XX
SQL
DELETE FROM ibf_conf_settings_titles WHERE conf_title_id = XX
Replace the XX in those queries with the number from above.
Next, it would be a good idea to update your settings cache by going into ACP -> Maintenance -> Cache Control, then click the update button on the settings cache row. Hope this helps.
Credit: FuSoYa