I use this daily and aside from the issue posted here:
I have a bad habbit of typing exit every time I'm done in a terminal here is my solution stole from the kuake style setup for urxvt and openbox.
Requires xdotool.
in ~/.local/bin/urxvtq ( or somewhere in your $PATH )
#!/bin/bash
wid=$(xdotool search --classname scratchpad_urxvt_top)
if [ -z "$wid" ]; then
#your prefered urxvt output here.
urxvt -pe default,matcher -name scratchpad_urxvt_top -geometry 180x28
fi
then in your .i3/config modify your bindsym for show/hide of the scratchpad window:
bindsym $mod+<key> exec .local/bin/urxvtq, [instance="scratchpad_urxvt_top"] scratchpad show, move position 45px 0px
Now if you close your scratchpad by mistake hit your chosen hotkey and a new window will be spawned!
Sadly it doesn't focus the window so you have to hit it twice, a small price to pay versus manually firing up a new window.