To close all windows except the frontmost window, run:

    osascript -e 'tell app "Google Chrome" to close (windows 2 thru -1)'

To close all windows except the window opened first, run a script like this in AppleScript Editor:
    
    tell application "Google Chrome"
        if number of windows < 2 then return
        set min to id of window 1
        repeat with w in windows 2 thru -1
            if id of w < min then set min to id of w
        end repeat
        close (windows where id is not min)
    end tell

"Instances" are usually called windows in OS X, and windows are not separate instances of a process like the instances opened by `open -n`.