I'm not sure if org-reset-checkbox-state-subtree is supposed to update the cookies, although that would seem logical.
However, C-u C-c # will incorrectly accumulate the checkbox entries from previous sections when updating the file, which is clearly a bug: *** Loose Papers [0/6]… *** Process Your Notes [0/9]… *** Empty Your Head [0/10]… *** Review Action Lists [0/11]… *** Review Waiting-For List [0/12]… *** Review Project (and Larger Outcome) Lists [0/15]… *** Review Previous Calendar Data [0/16]… *** Review Upcoming Calendar [0/17]… *** Review Any Relevant Checklists [0/18]… *** Be Creative and Courageous [0/19]… C-c # on an individual section entry does the right thing. Regards, Achim. -- +<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+ Wavetables for the Terratec KOMPLEXER: http://Synth.Stromeko.net/Downloads.html#KomplexerWaves