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This page tries to explain the "first window not restored" issue some users have reported.
TL;DR
tmux-resurrect respects windows and panes you manually open and never overrides them. When you start a new tmux session the first window is automatically created. Because it exists at the time of the restoration it will not be overridden.
Solution:
Do all the work in named sessions. That way there won't be anything to restore in the first window of a session named 0. Sessions can be named/renamed with prefix+$.