I got bored and wrote up a nav file generator for use on Windows.
I would not suggest using it on a desktop that is being used. Preferably it should be ran in a VM as to not cause issues with other programs while running.
On first run:
Where ever you place the generate.bat file you will need to place a copy of steamcmd.exe, if you do not have a copy of steamcmd.exe it will open your default browser to Valve's wiki page on steamcmd so you may downloaded directly from Valve. Once steam.exe is placed in same folder as generate.bat press enter (or if you have exited the NavGen console re-run generate.bat) and it will move and install steamcmd for you, after that it ask to download the SRCDS TF2 server that we will use to generate the nav files. Press enter and it will download the server. Once the server is installed it will open the maps folder for you to add your maps to. Once you add all your maps, press enter and it will start making .nav files for the maps you added.
After steamcmd and the srcds server has been added:
The batch file will automatically generate nav files for the maps in your maps folder that do not already have a .nav file.
GitHub
https://github.com/vman315/TF2-NavGenerator