The update only updates what's already there. This is different behavior than in previous releases. Maybe I should change it back to the way it was in a new release, I don't know. Anyway, to index the new section, just use the textbox. Note to a) set different values in the update sites table and choose yes or b) use the search depth and links per dropdowns and choose no. Otherwise, when you index/update, any values present in the update sites table will be used by default. You might also want to set LIMIT_TO_DIRECTORY to true in the config file to keep PhpDig within a directory, and there is
this thread that may be of interest too.