"|" pipe operator redirects I/O to a subshell.

Variables in a subshell are not visible outside the block of code in the subshell.

Thus the following code doesn’t work as intended.

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# check every window
all_closed=1
wmctrl -l | awk '{print $1}' | while read APP; do
    notify-send "[$APP] is not closed, please check unsaved content and close it manually."
    $all_closed=0
done

if [[ $all_closed -eq 0 ]]; then
    exit 2
fi

The all_closed variable is modified in the subshell created by pipes. The outside one remains unchanged. And the script will never exit with error code 2 no matter all windows are closed or not.

Fixing this piece of code is easy, just avoid using subshell (pipe).

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for APP in $(wmctrl -l | awk '{print $1}'); do
    notify-send "[$APP] is not closed, please check unsaved content and close it manually."
    $all_closed=0
done

References