Despite modifying the navigation pane's width the CHM file is not updated
You change the navigation tab's width in the HelpNDoc's projects settings but when opening the CHM file, nothing has changed.
The Microsoft HTML help viewer stores the help window's size and position for each individual help file as soon as it has been launched. Modifying the help settings after that won't have any effect as the help viewer will only read local configuration for that help file and ignore the file's settings set up using HelpNDoc.
A solution would be to erase the help viewer's configuration file, but be warned that this file contains all the configuration made to all the help files viewed on the system. So deleting this file will delete the configuration options for all the other files too.
This file is usually located there: C:\Users\%username%\AppData\Roaming\Microsoft\HTML Help\hh.dat where %username% is your Windows user name.