Finally tracked down and came up with a work around for that weird bug. Sometimes i3's input gets into a weird state, I think because some windows either don't close properly or move the focus somewhere it shouldn't be. Either way it breaks keyboard input completely even though i3 itself is fine. Added a watchdog to check for this condition and reset i3 if it happens. Sure, your desktop may pop up but it beats the hell out of a frozen GUI.

i38.sh

@@ -1149,6 +1149,10 @@ $(if [[ $sounds -eq 0 ]]; then
         echo "exec_always --no-startup-id ${i3Path}/scripts/sound.py"
     fi
 fi
+# i3 watchdog - monitors i3 responsiveness and auto-recovers from freezes
+if [[ $usingSway -ne 0 ]]; then
+    echo "exec_always --no-startup-id ${i3Path}/scripts/i3_watchdog.sh"
+fi
 # xbrlapi is X11-only, skip on Sway/Wayland
 if [[ $brlapi -eq 0 ]] && [[ $usingSway -ne 0 ]]; then
     echo 'exec --no-startup-id xbrlapi --quiet'