I noticed the one provided was not only named incorrectly (and so would not function, as the nav file I'm pretty sure needs to be the same name as the .bsp file), looking like it was created from a decompile of free2fort instead of the original .bsp, and also I found areas where there was no nav meshes, meaning bots could not traverse them, including the top of blue base where a spawn room is. Any bots that would spawn up there would never move as there was no nav present.
I slapped down nav_mark_walkable points throughout all the areas in the map I could locate which did not have nav meshes and generated the entire .nav again. Bots now are able to traverse all areas in the map properly. Here is a link to the improved (and correctly named) .nav file I generated and made sure nav meshes were present in all walkable areas including obscure rooftops.
https://www.dropbox.com/s/mycbs8qnn3pajba/ctf_free2fort.nav?dl=0
I really love this idea of a map, with all these extra hidey holes and sneaky places. Hope it gets updated to resolve that annoying clipping plane issue with the fog_controller. It's quite off-putting for snipers way up high. I also hope red base gets way more detail and sneaky back-area stuff like blue base has with the mining tunnel.
Edit: Improved nav file even further. Discovered bots couldn't go up stairs, only down, found a couple places I missed that had no nav meshes, added manual nav mesh modification for more complex navigation to allow bots to get up on top of blue silos, which currently was only possible via jumping from barn roof on to a pipe, which the bots now know how to do.