The sites (credentials and alike) should not be present in the INI file after you have deleted it in GUI.

Though as @Mayhem posted, some caches (visited paths and hostkeys) may still be present. They are not really related to the stored sites. The caches are stored, even if you open an ad hoc connection.

What I did was make a backup of the config file, then manually edited it.

After emptying the CDCache, Banners and LastFingerprints sections, my config file went from 197K to 26K. Then I exported the settings file, and it reduced the file even further to 19.5K.

I was trying to resolve a problem with not opening local directories as listed for each site so was poking around in the settings .ini file

I was shocked to find that it was full of really old sites that have not been active for several years despite having deleted them in the interface.

What is the correct way to remove a site that will also clean it out of the .ini file?

Do I have to risk manual editing of this whole file for obsolete entries?

Shouldn't the be removed when a site is deleted?